	title	geo_accession	status	submission_date	last_update_date	type	channel_count	source_name_ch1	organism_ch1	characteristics_ch1	characteristics_ch1.1	characteristics_ch1.2	characteristics_ch1.3	treatment_protocol_ch1	treatment_protocol_ch1.1	growth_protocol_ch1	molecule_ch1	extract_protocol_ch1	label_ch1	label_protocol_ch1	taxid_ch1	source_name_ch2	organism_ch2	characteristics_ch2	characteristics_ch2.1	treatment_protocol_ch2	treatment_protocol_ch2.1	growth_protocol_ch2	molecule_ch2	extract_protocol_ch2	label_ch2	label_protocol_ch2	taxid_ch2	hyb_protocol	scan_protocol	description	data_processing	platform_id	contact_name	contact_email	contact_phone	contact_laboratory	contact_department	contact_institute	contact_address	contact_city	contact_state	contact_zip/postal_code	contact_country	supplementary_file	data_row_count	cell type:ch1	cell type:ch2	dose:ch1	time:ch1	treatment:ch1	treatment:ch2
GSM862576	200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4a	GSM862576	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 4 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862576/suppl/GSM862576_7748E1_251485060682_S01_GE2-v5.1_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	4 hr incubation	200 nm SiO2 worms	media control
GSM862577	200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4b	GSM862577	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 4 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862577/suppl/GSM862577_7748E2_251485060682_S01_GE2-v5.1_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	4 hr incubation	200 nm SiO2 worms	media control
GSM862578	200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4c	GSM862578	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 4 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862578/suppl/GSM862578_7748E3_251485060682_S01_GE2-v5.1_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	4 hr incubation	200 nm SiO2 worms	media control
GSM862579	200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24a	GSM862579	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 24 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862579/suppl/GSM862579_7748E4_251485060682_S01_GE2-v5.1_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	24 hr incubation	200 nm SiO2 worms	media control
GSM862580	200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24b	GSM862580	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 24 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862580/suppl/GSM862580_7748E5_251485060683_S01_GE2-v5.1_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	24 hr incubation	200 nm SiO2 worms	media control
GSM862581	200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4a	GSM862581	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 4 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862581/suppl/GSM862581_7748E6_251485060683_S01_GE2-v5.1_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	4 hr incubation	200 nm SiO2 spheres	media control
GSM862582	200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4b	GSM862582	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 4 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862582/suppl/GSM862582_7748E7_251485060683_S01_GE2-v5.1_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	4 hr incubation	200 nm SiO2 spheres	media control
GSM862583	200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4c	GSM862583	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 4 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862583/suppl/GSM862583_7748E8_251485060683_S01_GE2-v5.1_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	4 hr incubation	200 nm SiO2 spheres	media control
GSM862584	200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24c	GSM862584	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 24 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862584/suppl/GSM862584_7859E20_251485060576_S01_GE2-v5.2_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	24 hr incubation	200 nm SiO2 worms	media control
GSM862585	200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4a	GSM862585	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 4 hr incubation	dose: 73.38 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862585/suppl/GSM862585_7859E1_251485060572_S01_GE2-v5.2_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	73.38 ug/ml	4 hr incubation	200 nm SiO2 spheres	media control
GSM862586	200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4b	GSM862586	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 4 hr incubation	dose: 73.38 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862586/suppl/GSM862586_7859E1E4_251485060572_S01_GE2-v5.2_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	73.38 ug/ml	4 hr incubation	200 nm SiO2 spheres	media control
GSM862587	200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4c	GSM862587	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 4 hr incubation	dose: 73.38 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862587/suppl/GSM862587_7859E3_251485060572_S01_GE2-v5.2_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	73.38 ug/ml	4 hr incubation	200 nm SiO2 spheres	media control
GSM862588	200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24a	GSM862588	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 24 hr incubation	dose: 73.38 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862588/suppl/GSM862588_7859E4_251485060572_S01_GE2-v5.2_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	73.38 ug/ml	24 hr incubation	200 nm SiO2 spheres	media control
GSM862589	200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24b	GSM862589	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 24 hr incubation	dose: 73.38 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862589/suppl/GSM862589_7859E5_251485060573_S01_GE2-v5.2_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	73.38 ug/ml	24 hr incubation	200 nm SiO2 spheres	media control
GSM862590	200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24c	GSM862590	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 sphere	Homo sapiens	time: 24 hr incubation	dose: 73.38 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 spheres	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862590/suppl/GSM862590_7859E6_251485060573_S01_GE2-v5.2_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	73.38 ug/ml	24 hr incubation	200 nm SiO2 spheres	media control
GSM862591	G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4a	GSM862591	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G3.5-COOH dendrimer	Homo sapiens	time: 4 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G3.5-COOH PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862591/suppl/GSM862591_7859E7_251485060573_S01_GE2-v5.2_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	4 hr incubation	G3.5-COOH PAMAM	media control
GSM862592	G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4b	GSM862592	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G3.5-COOH dendrimer	Homo sapiens	time: 4 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G3.5-COOH PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862592/suppl/GSM862592_7859E8_251485060573_S01_GE2-v5.2_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	4 hr incubation	G3.5-COOH PAMAM	media control
GSM862593	G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4c	GSM862593	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G3.5-COOH dendrimer	Homo sapiens	time: 4 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G3.5-COOH PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862593/suppl/GSM862593_7859E9_251485060574_S01_GE2-v5.2_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	4 hr incubation	G3.5-COOH PAMAM	media control
GSM862594	G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24a	GSM862594	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G3.5-COOH dendrimer	Homo sapiens	time: 24 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G3.5-COOH PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862594/suppl/GSM862594_7859E10_251485060574_S01_GE2-v5.2_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	24 hr incubation	G3.5-COOH PAMAM	media control
GSM862595	G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24b	GSM862595	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G3.5-COOH dendrimer	Homo sapiens	time: 24 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G3.5-COOH PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862595/suppl/GSM862595_7859E11_251485060574_S01_GE2-v5.2_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	24 hr incubation	G3.5-COOH PAMAM	media control
GSM862596	G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24c	GSM862596	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G3.5-COOH dendrimer	Homo sapiens	time: 24 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G3.5-COOH PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862596/suppl/GSM862596_7859E12_251485060574_S01_GE2-v5.2_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	24 hr incubation	G3.5-COOH PAMAM	media control
GSM862597	G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4a	GSM862597	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G4-NH2 dendrimer	Homo sapiens	time: 4 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G4-NH2 PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862597/suppl/GSM862597_7859E13_251485060575_S01_GE2-v5.2_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	4 hr incubation	G4-NH2 PAMAM	media control
GSM862598	G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4b	GSM862598	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G4-NH2 dendrimer	Homo sapiens	time: 4 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G4-NH2 PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862598/suppl/GSM862598_7859E14_251485060575_S01_GE2-v5.2_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	4 hr incubation	G4-NH2 PAMAM	media control
GSM862599	G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4c	GSM862599	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G4-NH2 dendrimer	Homo sapiens	time: 4 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G4-NH2 PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862599/suppl/GSM862599_7859E15_251485060575_S01_GE2-v5.2_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	4 hr incubation	G4-NH2 PAMAM	media control
GSM862600	G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24a	GSM862600	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G4-NH2 dendrimer	Homo sapiens	time: 24 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G4-NH2 PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24a	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862600/suppl/GSM862600_7859E16_251485060575_S01_GE2-v5.2_10_Apr08_2_1_4.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	24 hr incubation	G4-NH2 PAMAM	media control
GSM862601	G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24b	GSM862601	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G4-NH2 dendrimer	Homo sapiens	time: 24 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G4-NH2 PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24b	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862601/suppl/GSM862601_7859E17_251485060576_S01_GE2-v5.2_10_Apr08_2_1_1.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	24 hr incubation	G4-NH2 PAMAM	media control
GSM862602	G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24c	GSM862602	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC G4-NH2 dendrimer	Homo sapiens	time: 24 hr incubation	dose: 0.5 uM	cell type: Primary human aortic endothial cells	treatment: G4-NH2 PAMAM	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24c	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862602/suppl/GSM862602_7859E18_251485060576_S01_GE2-v5.2_10_Apr08_2_1_2.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	0.5 uM	24 hr incubation	G4-NH2 PAMAM	media control
GSM862603	200 nm SiO2 worms 1.5 hr incubation 100 ug/ml nSiO2_W1.5	GSM862603	Public on Dec 20 2013	Jan 17 2012	Dec 20 2013	RNA	2	HAEC nSiO2 worm	Homo sapiens	time: 1.5 hr incubation	dose: 100 ug/ml	cell type: Primary human aortic endothial cells	treatment: 200 nm SiO2 worms	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy5	Agilent two-color LRILAK labeling protocol	9606	HAEC untreated control	Homo sapiens	treatment: media control	cell type: Primary human aortic endothial cells	The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.	For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.	All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.	total RNA	Total RNA was collected using Qiagen RNeasy Mini kits.	Cy3	Agilent two-color LRILAK labeling protocol	9606	Agilent two-color GE hyb/wash protocol	Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802	200 nm SiO2 worms 1.5 hr incubation 100 ug/ml nSiO2_W1.5	Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted	GPL4133	Philip,J,Moos	philip.moos@utah.edu	801-585-5952	Moos	Pharmacology & Toxicology	University of Utah	30 S 2000 East, Rm 201	Salt Lake City	UT	84112	USA	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862603/suppl/GSM862603_7859E19_251485060576_S01_GE2-v5.2_10_Apr08_2_1_3.txt.gz	45015	Primary human aortic endothial cells	Primary human aortic endothial cells	100 ug/ml	1.5 hr incubation	200 nm SiO2 worms	media control
