Result

Search results for the GEO ID: GSE31668

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM786182

GPL1355

AVIC sample#1 treated with DAPT

aortic valve cells treated with DAPT

strain: Sprague-Dawley cell type: aortic valve interstitial cells

Gene expression data from DAPT treated mouse replicate 1

Sample_geo_accession	GSM786182
Sample_status	Public on Aug 26 2011
Sample_submission_date	Aug 25 2011
Sample_last_update_date	Aug 26 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin. Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA. AVICs between passage 3 and 8 were used for experiments. Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_hyb_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_scan_protocol	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_data_processing	Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA). Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.
Sample_platform_id	GPL1355
Sample_contact_name	Vidu,,Garg
Sample_contact_email	vidu.garg@nationwidechildrens.org
Sample_contact_phone	614-355-3091
Sample_contact_fax	614-722-4881
Sample_contact_laboratory	Vidu Garg
Sample_contact_department	Cardiovascular and Pulmonary Research
Sample_contact_institute	Research Institute at Nationwide Children's Hospital
Sample_contact_address	700 Children's Drive W302
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43205
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786182/suppl/GSM786182_DAPT1.CEL.gz
Sample_series_id	GSE31668
Sample_data_row_count	31099

GSM786183

GPL1355

AVIC sample#2 treated with DAPT

aortic valve cells treated with DAPT

strain: Sprague-Dawley cell type: aortic valve interstitial cells

Gene expression data from DAPT treated mouse replicate 2

Sample_geo_accession	GSM786183
Sample_status	Public on Aug 26 2011
Sample_submission_date	Aug 25 2011
Sample_last_update_date	Aug 26 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin. Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA. AVICs between passage 3 and 8 were used for experiments. Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_hyb_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_scan_protocol	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_data_processing	Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA). Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.
Sample_platform_id	GPL1355
Sample_contact_name	Vidu,,Garg
Sample_contact_email	vidu.garg@nationwidechildrens.org
Sample_contact_phone	614-355-3091
Sample_contact_fax	614-722-4881
Sample_contact_laboratory	Vidu Garg
Sample_contact_department	Cardiovascular and Pulmonary Research
Sample_contact_institute	Research Institute at Nationwide Children's Hospital
Sample_contact_address	700 Children's Drive W302
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43205
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786183/suppl/GSM786183_DAPT2.CEL.gz
Sample_series_id	GSE31668
Sample_data_row_count	31099

GSM786184

GPL1355

AVIC sample#3 treated with DAPT

aortic valve cells treated with DAPT

strain: Sprague-Dawley cell type: aortic valve interstitial cells

Gene expression data from DAPT treated mouse replicate 3

Sample_geo_accession	GSM786184
Sample_status	Public on Aug 26 2011
Sample_submission_date	Aug 25 2011
Sample_last_update_date	Aug 26 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin. Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA. AVICs between passage 3 and 8 were used for experiments. Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_hyb_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_scan_protocol	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_data_processing	Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA). Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.
Sample_platform_id	GPL1355
Sample_contact_name	Vidu,,Garg
Sample_contact_email	vidu.garg@nationwidechildrens.org
Sample_contact_phone	614-355-3091
Sample_contact_fax	614-722-4881
Sample_contact_laboratory	Vidu Garg
Sample_contact_department	Cardiovascular and Pulmonary Research
Sample_contact_institute	Research Institute at Nationwide Children's Hospital
Sample_contact_address	700 Children's Drive W302
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43205
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786184/suppl/GSM786184_DAPT3.CEL.gz
Sample_series_id	GSE31668
Sample_data_row_count	31099

GSM786185

GPL1355

AVIC sample#1 treated with DMSO

aortic valve cells treated with DMSO

strain: Sprague-Dawley cell type: aortic valve interstitial cells

Gene expression data from DMSO treated mouse replicate 1

Sample_geo_accession	GSM786185
Sample_status	Public on Aug 26 2011
Sample_submission_date	Aug 25 2011
Sample_last_update_date	Aug 26 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin. Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA. AVICs between passage 3 and 8 were used for experiments. Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_hyb_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_scan_protocol	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_data_processing	Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA). Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.
Sample_platform_id	GPL1355
Sample_contact_name	Vidu,,Garg
Sample_contact_email	vidu.garg@nationwidechildrens.org
Sample_contact_phone	614-355-3091
Sample_contact_fax	614-722-4881
Sample_contact_laboratory	Vidu Garg
Sample_contact_department	Cardiovascular and Pulmonary Research
Sample_contact_institute	Research Institute at Nationwide Children's Hospital
Sample_contact_address	700 Children's Drive W302
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43205
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786185/suppl/GSM786185_DMSO1.CEL.gz
Sample_series_id	GSE31668
Sample_data_row_count	31099

GSM786186

GPL1355

AVIC sample#2 treated with DMSO

aortic valve cells treated with DMSO

strain: Sprague-Dawley cell type: aortic valve interstitial cells

Gene expression data from DMSO treated mouse replicate 2

Sample_geo_accession	GSM786186
Sample_status	Public on Aug 26 2011
Sample_submission_date	Aug 25 2011
Sample_last_update_date	Aug 26 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin. Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA. AVICs between passage 3 and 8 were used for experiments. Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_hyb_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_scan_protocol	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_data_processing	Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA). Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.
Sample_platform_id	GPL1355
Sample_contact_name	Vidu,,Garg
Sample_contact_email	vidu.garg@nationwidechildrens.org
Sample_contact_phone	614-355-3091
Sample_contact_fax	614-722-4881
Sample_contact_laboratory	Vidu Garg
Sample_contact_department	Cardiovascular and Pulmonary Research
Sample_contact_institute	Research Institute at Nationwide Children's Hospital
Sample_contact_address	700 Children's Drive W302
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43205
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786186/suppl/GSM786186_DMSO2.CEL.gz
Sample_series_id	GSE31668
Sample_data_row_count	31099

GSM786187

GPL1355

AVIC sample#3 treated with DMSO

aortic valve cells treated with DMSO

strain: Sprague-Dawley cell type: aortic valve interstitial cells

Gene expression data from DMSO treated mouse replicate 3

Sample_geo_accession	GSM786187
Sample_status	Public on Aug 26 2011
Sample_submission_date	Aug 25 2011
Sample_last_update_date	Aug 26 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin. Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA. AVICs between passage 3 and 8 were used for experiments. Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Sample_hyb_protocol	GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
Sample_scan_protocol	CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.
Sample_data_processing	Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA). Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.
Sample_platform_id	GPL1355
Sample_contact_name	Vidu,,Garg
Sample_contact_email	vidu.garg@nationwidechildrens.org
Sample_contact_phone	614-355-3091
Sample_contact_fax	614-722-4881
Sample_contact_laboratory	Vidu Garg
Sample_contact_department	Cardiovascular and Pulmonary Research
Sample_contact_institute	Research Institute at Nationwide Children's Hospital
Sample_contact_address	700 Children's Drive W302
Sample_contact_city	Columbus
Sample_contact_state	OH
Sample_contact_zip/postal_code	43205
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786187/suppl/GSM786187_DMSO3.CEL.gz
Sample_series_id	GSE31668
Sample_data_row_count	31099

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