Result

Search results for the GEO ID: GSE46116

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM1123917

GPL1261

Untreated r1

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: untreated cell line: 7438 cells

Untreated cells - replicate 1

Sample_geo_accession	GSM1123917
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123917/suppl/GSM1123917_1_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123917/suppl/GSM1123917_1_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123918

GPL1261

Untreated r2

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: untreated cell line: 7438 cells

Untreated cells - replicate 2

Sample_geo_accession	GSM1123918
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123918/suppl/GSM1123918_5_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123918/suppl/GSM1123918_5_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123919

GPL1261

Dex (2h) r1

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: Dexamethasone for 2 hours cell line: 7438 cells

Cells treated with Dex - replicate 1

Sample_geo_accession	GSM1123919
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123919/suppl/GSM1123919_2_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123919/suppl/GSM1123919_2_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123920

GPL1261

Dex (2h) r2

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: Dexamethasone for 2 hours cell line: 7438 cells

Cells treated with Dex - replicate 2

Sample_geo_accession	GSM1123920
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123920/suppl/GSM1123920_6_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123920/suppl/GSM1123920_6_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123921

GPL1261

E2 (2h) r1

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: Estradiol for 2 hours cell line: 7438 cells

Cells treated with E2 - replicate 1

Sample_geo_accession	GSM1123921
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123921/suppl/GSM1123921_3_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123921/suppl/GSM1123921_3_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123922

GPL1261

E2 (2h) r2

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: Estradiol for 2 hours cell line: 7438 cells

GR-ChIP in cells treated with E2 - replicate 2

Sample_geo_accession	GSM1123922
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123922/suppl/GSM1123922_7_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123922/suppl/GSM1123922_7_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123923

GPL1261

Dex + E2 (2h) r1

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: Dexamethasone + Estradiol for 2 hours cell line: 7438 cells

GR-ChIP in cells treated with Dex + E2 - replicate 1

Sample_geo_accession	GSM1123923
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123923/suppl/GSM1123923_4_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123923/suppl/GSM1123923_4_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

GSM1123924

GPL1261

Dex + E2 (2h) r2

7438 cells

cell type: mouse mammary cells (express GFP-GR and Cherry-ER under a tet regulated promoter) treatment: Dexamethasone + Estradiol for 2 hours cell line: 7438 cells

Cells treated with Dex + E2 - replicate 2

Sample_geo_accession	GSM1123924
Sample_status	Public on Jul 01 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 2 hours.
Sample_growth_protocol_ch1	For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells were harvested in trizol and then extracted with chloroform. Samples were then further purified using the Qiagen RNA purification kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were processed, labeled, hybridized, and scanned at the Frederick National Laboratory for Cancer Research Microarray Core using standard procedures.
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	Affymetrix Mouse Genome 430 2.0 array data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA’ and its quantile normalization method. Mean expression values from biological duplicates were calculated.
Sample_platform_id	GPL1261
Sample_contact_name	Songjoon,,Baek
Sample_contact_laboratory	LRBGE
Sample_contact_department	CCR
Sample_contact_institute	NCI / NIH
Sample_contact_address	41 Library Drive
Sample_contact_city	Bethesda
Sample_contact_state	MD
Sample_contact_zip/postal_code	20892
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123924/suppl/GSM1123924_8_Mouse430_2_.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123924/suppl/GSM1123924_8_Mouse430_2_.rma.chp.gz
Sample_series_id	GSE46116
Sample_series_id	GSE46124
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes