Result

Search results for the GEO ID: GSE15065

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GSM ID

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Title

Source name

Description

Characteristics

GSM376944

GPL570

MCF10A cells with C/EBPbeta-2; biological rep 1

MCF10A cells with C/EBPbeta-2

cell line: MCF10A cells

gene expression

Sample_geo_accession	GSM376944
Sample_status	Public on Mar 02 2010
Sample_submission_date	Mar 02 2009
Sample_last_update_date	Mar 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	none
Sample_growth_protocol_ch1	Cells were grown in a 1:1 mixture of Dulbecco’s modified Eagle medium (DMEM) and Ham’s F12 containing 2.5 mM L-glutamine and supplemented with 5% horse serum (Sigma, St. Louis MO), 10 micrograms/ml recombinant human insulin (Invitrogen Corp., Grand Island NY), 0.5 micrograms/ml hydrocortisone, 10 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 50 U/ml penicillin, and 50 micrograms/ml streptomycin.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy Mini kit and RNase-Free DNase kit (Qiagen)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides
Sample_hyb_protocol	The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Genome Plus 2.0 Array containing 54,000 sets of 11 to 25-mer oligomers, representing 47,000 mouse transcripts (38,500 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.
Sample_scan_protocol	GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
Sample_data_processing	Three independent replicates were performed to allow for statistical analysis. CEL files were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis) (Bolstad et al., 2003). All probesets showing at least a 2 fold change in one of the C/EBPbeta-2 overexpressing MCF10A cells compared to parental MCF10A were tested with a Welch’s t-test and a p-value cutoff of 0.05. This restriction tested 3,721 genes. As a result 443 genes were found to be differentially expressed upon C/EBPbeta-2 overexpression in MCF10A cells. Of these differentially expressed genes, 86 were found to be upregulated 2 fold or more while 121 were found to be downregulated 2 fold or more.
Sample_platform_id	GPL570
Sample_contact_name	Linda,J,Sealy
Sample_contact_email	Linda.Sealy@Vanderbilt.edu
Sample_contact_phone	(615) 322-7024
Sample_contact_laboratory	Sealy Lab
Sample_contact_department	Cancer Biology
Sample_contact_institute	Vanderbilt University Medical Center
Sample_contact_address	2202 Pierce Ave
Sample_contact_city	Nashville
Sample_contact_state	TN
Sample_contact_zip/postal_code	37232
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM376nnn/GSM376944/suppl/GSM376944.CEL.gz
Sample_series_id	GSE15065
Sample_data_row_count	54675

GSM376945

GPL570

MCF10A cells with C/EBPbeta-2; biological rep 2

MCF10A cells with C/EBPbeta-2

cell line: MCF10A cells

gene expression

Sample_geo_accession	GSM376945
Sample_status	Public on Mar 02 2010
Sample_submission_date	Mar 02 2009
Sample_last_update_date	Mar 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	none
Sample_growth_protocol_ch1	Cells were grown in a 1:1 mixture of Dulbecco’s modified Eagle medium (DMEM) and Ham’s F12 containing 2.5 mM L-glutamine and supplemented with 5% horse serum (Sigma, St. Louis MO), 10 micrograms/ml recombinant human insulin (Invitrogen Corp., Grand Island NY), 0.5 micrograms/ml hydrocortisone, 10 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 50 U/ml penicillin, and 50 micrograms/ml streptomycin.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy Mini kit and RNase-Free DNase kit (Qiagen)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides
Sample_hyb_protocol	The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Genome Plus 2.0 Array containing 54,000 sets of 11 to 25-mer oligomers, representing 47,000 mouse transcripts (38,500 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.
Sample_scan_protocol	GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
Sample_data_processing	Three independent replicates were performed to allow for statistical analysis. CEL files were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis) (Bolstad et al., 2003). All probesets showing at least a 2 fold change in one of the C/EBPbeta-2 overexpressing MCF10A cells compared to parental MCF10A were tested with a Welch’s t-test and a p-value cutoff of 0.05. This restriction tested 3,721 genes. As a result 443 genes were found to be differentially expressed upon C/EBPbeta-2 overexpression in MCF10A cells. Of these differentially expressed genes, 86 were found to be upregulated 2 fold or more while 121 were found to be downregulated 2 fold or more.
Sample_platform_id	GPL570
Sample_contact_name	Linda,J,Sealy
Sample_contact_email	Linda.Sealy@Vanderbilt.edu
Sample_contact_phone	(615) 322-7024
Sample_contact_laboratory	Sealy Lab
Sample_contact_department	Cancer Biology
Sample_contact_institute	Vanderbilt University Medical Center
Sample_contact_address	2202 Pierce Ave
Sample_contact_city	Nashville
Sample_contact_state	TN
Sample_contact_zip/postal_code	37232
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM376nnn/GSM376945/suppl/GSM376945.CEL.gz
Sample_series_id	GSE15065
Sample_data_row_count	54675

GSM376946

GPL570

MCF10A cells with C/EBPbeta-2; biological rep 3

MCF10A cells with C/EBPbeta-2

cell line: MCF10A cells

gene expression

Sample_geo_accession	GSM376946
Sample_status	Public on Mar 02 2010
Sample_submission_date	Mar 02 2009
Sample_last_update_date	Mar 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	none
Sample_growth_protocol_ch1	Cells were grown in a 1:1 mixture of Dulbecco’s modified Eagle medium (DMEM) and Ham’s F12 containing 2.5 mM L-glutamine and supplemented with 5% horse serum (Sigma, St. Louis MO), 10 micrograms/ml recombinant human insulin (Invitrogen Corp., Grand Island NY), 0.5 micrograms/ml hydrocortisone, 10 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 50 U/ml penicillin, and 50 micrograms/ml streptomycin.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy Mini kit and RNase-Free DNase kit (Qiagen)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides
Sample_hyb_protocol	The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Genome Plus 2.0 Array containing 54,000 sets of 11 to 25-mer oligomers, representing 47,000 mouse transcripts (38,500 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.
Sample_scan_protocol	GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
Sample_data_processing	Three independent replicates were performed to allow for statistical analysis. CEL files were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis) (Bolstad et al., 2003). All probesets showing at least a 2 fold change in one of the C/EBPbeta-2 overexpressing MCF10A cells compared to parental MCF10A were tested with a Welch’s t-test and a p-value cutoff of 0.05. This restriction tested 3,721 genes. As a result 443 genes were found to be differentially expressed upon C/EBPbeta-2 overexpression in MCF10A cells. Of these differentially expressed genes, 86 were found to be upregulated 2 fold or more while 121 were found to be downregulated 2 fold or more.
Sample_platform_id	GPL570
Sample_contact_name	Linda,J,Sealy
Sample_contact_email	Linda.Sealy@Vanderbilt.edu
Sample_contact_phone	(615) 322-7024
Sample_contact_laboratory	Sealy Lab
Sample_contact_department	Cancer Biology
Sample_contact_institute	Vanderbilt University Medical Center
Sample_contact_address	2202 Pierce Ave
Sample_contact_city	Nashville
Sample_contact_state	TN
Sample_contact_zip/postal_code	37232
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM376nnn/GSM376946/suppl/GSM376946.CEL.gz
Sample_series_id	GSE15065
Sample_data_row_count	54675

GSM376947

GPL570

MCF10A cells; biological rep 1

MCF10A cells

cell line: MCF10A cells

gene expression

Sample_geo_accession	GSM376947
Sample_status	Public on Mar 02 2010
Sample_submission_date	Mar 02 2009
Sample_last_update_date	Mar 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	none
Sample_growth_protocol_ch1	Cells were grown in a 1:1 mixture of Dulbecco’s modified Eagle medium (DMEM) and Ham’s F12 containing 2.5 mM L-glutamine and supplemented with 5% horse serum (Sigma, St. Louis MO), 10 micrograms/ml recombinant human insulin (Invitrogen Corp., Grand Island NY), 0.5 micrograms/ml hydrocortisone, 10 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 50 U/ml penicillin, and 50 micrograms/ml streptomycin.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy Mini kit and RNase-Free DNase kit (Qiagen)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides
Sample_hyb_protocol	The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Genome Plus 2.0 Array containing 54,000 sets of 11 to 25-mer oligomers, representing 47,000 mouse transcripts (38,500 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.
Sample_scan_protocol	GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
Sample_data_processing	Three independent replicates were performed to allow for statistical analysis. CEL files were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis) (Bolstad et al., 2003). All probesets showing at least a 2 fold change in one of the C/EBPbeta-2 overexpressing MCF10A cells compared to parental MCF10A were tested with a Welch’s t-test and a p-value cutoff of 0.05. This restriction tested 3,721 genes. As a result 443 genes were found to be differentially expressed upon C/EBPbeta-2 overexpression in MCF10A cells. Of these differentially expressed genes, 86 were found to be upregulated 2 fold or more while 121 were found to be downregulated 2 fold or more.
Sample_platform_id	GPL570
Sample_contact_name	Linda,J,Sealy
Sample_contact_email	Linda.Sealy@Vanderbilt.edu
Sample_contact_phone	(615) 322-7024
Sample_contact_laboratory	Sealy Lab
Sample_contact_department	Cancer Biology
Sample_contact_institute	Vanderbilt University Medical Center
Sample_contact_address	2202 Pierce Ave
Sample_contact_city	Nashville
Sample_contact_state	TN
Sample_contact_zip/postal_code	37232
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM376nnn/GSM376947/suppl/GSM376947.CEL.gz
Sample_series_id	GSE15065
Sample_data_row_count	54675

GSM376949

GPL570

MCF10A cells; biological rep 3

MCF10A cells

cell line: MCF10A cells

gene expression

Sample_geo_accession	GSM376949
Sample_status	Public on Mar 02 2010
Sample_submission_date	Mar 02 2009
Sample_last_update_date	Mar 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	none
Sample_growth_protocol_ch1	Cells were grown in a 1:1 mixture of Dulbecco’s modified Eagle medium (DMEM) and Ham’s F12 containing 2.5 mM L-glutamine and supplemented with 5% horse serum (Sigma, St. Louis MO), 10 micrograms/ml recombinant human insulin (Invitrogen Corp., Grand Island NY), 0.5 micrograms/ml hydrocortisone, 10 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 50 U/ml penicillin, and 50 micrograms/ml streptomycin.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy Mini kit and RNase-Free DNase kit (Qiagen)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides
Sample_hyb_protocol	The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Genome Plus 2.0 Array containing 54,000 sets of 11 to 25-mer oligomers, representing 47,000 mouse transcripts (38,500 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.
Sample_scan_protocol	GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
Sample_data_processing	Three independent replicates were performed to allow for statistical analysis. CEL files were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis) (Bolstad et al., 2003). All probesets showing at least a 2 fold change in one of the C/EBPbeta-2 overexpressing MCF10A cells compared to parental MCF10A were tested with a Welch’s t-test and a p-value cutoff of 0.05. This restriction tested 3,721 genes. As a result 443 genes were found to be differentially expressed upon C/EBPbeta-2 overexpression in MCF10A cells. Of these differentially expressed genes, 86 were found to be upregulated 2 fold or more while 121 were found to be downregulated 2 fold or more.
Sample_platform_id	GPL570
Sample_contact_name	Linda,J,Sealy
Sample_contact_email	Linda.Sealy@Vanderbilt.edu
Sample_contact_phone	(615) 322-7024
Sample_contact_laboratory	Sealy Lab
Sample_contact_department	Cancer Biology
Sample_contact_institute	Vanderbilt University Medical Center
Sample_contact_address	2202 Pierce Ave
Sample_contact_city	Nashville
Sample_contact_state	TN
Sample_contact_zip/postal_code	37232
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM376nnn/GSM376949/suppl/GSM376949.CEL.gz
Sample_series_id	GSE15065
Sample_data_row_count	54675

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