Result

Search results for the GEO ID: GSE28681

(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

GSM710379

GPL570

24hi_a

24hi

cell line: HMLE cell type: epithelial subpopulations

gene expression of immortalized human mammary epithelial cells positively sorted for CD24 expression

Sample_geo_accession	GSM710379
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710379/suppl/GSM710379_01_HMLE-24hi_a.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710379/suppl/GSM710379_01_HMLE-24hi_a.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710380

GPL570

msp1_a

msp1

cell line: HMLE cell type: mesenchymal subpopulations

gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

Sample_geo_accession	GSM710380
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710380/suppl/GSM710380_02_HMLE-msp1_a.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710380/suppl/GSM710380_02_HMLE-msp1_a.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710381

GPL570

msp2_a

msp2

cell line: HMLE cell type: mesenchymal subpopulations

gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

Sample_geo_accession	GSM710381
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710381/suppl/GSM710381_03_HMLE-msp2_a.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710381/suppl/GSM710381_03_HMLE-msp2_a.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710382

GPL570

msp3_a

msp3

cell line: HMLE cell type: mesenchymal subpopulations

gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

Sample_geo_accession	GSM710382
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710382/suppl/GSM710382_04_HMLE-msp3_a.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710382/suppl/GSM710382_04_HMLE-msp3_a.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710383

GPL570

24hi_b

24hi

cell line: HMLE cell type: epithelial subpopulations

gene expression of immortalized human mammary epithelial cells positively sorted for CD24 expression

Sample_geo_accession	GSM710383
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710383/suppl/GSM710383_05_HMLE-24hi_b.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710383/suppl/GSM710383_05_HMLE-24hi_b.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710384

GPL570

msp1_b

msp1

cell line: HMLE cell type: mesenchymal subpopulations

gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

Sample_geo_accession	GSM710384
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710384/suppl/GSM710384_06_HMLE-msp1_b.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710384/suppl/GSM710384_06_HMLE-msp1_b.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710385

GPL570

msp2_b

msp2

cell line: HMLE cell type: mesenchymal subpopulations

gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

Sample_geo_accession	GSM710385
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710385/suppl/GSM710385_07_HMLE-msp2_b.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710385/suppl/GSM710385_07_HMLE-msp2_b.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

GSM710386

GPL570

msp3_b

msp3

cell line: HMLE cell type: mesenchymal subpopulations

gene expression of a mesenchymal subpopulation within immortalized human mammary epithelial cells

Sample_geo_accession	GSM710386
Sample_status	Public on Apr 19 2011
Sample_submission_date	Apr 18 2011
Sample_last_update_date	Apr 19 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	HMLE cells and their derivatives were cultured in MEGM medium (Lonza) under standard conditions
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen total RNA extraction kit was used according to manufacturer's protocols.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_hyb_protocol	GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Sample_scan_protocol	Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	Arrays were analyzed using GeneChip Expression Console. Differences in gene expression between 24hi and the 3 msp cell lines were assayed using Limma software according to standard protocols. A table containing the resultant 3 pairwise comparisons also providing probe identities is linked to the Series record as a supplementary file.
Sample_platform_id	GPL570
Sample_contact_name	Christina,,Scheel
Sample_contact_laboratory	Weinberg
Sample_contact_institute	Whitehead Institute for Biomedical Research
Sample_contact_address	9 Cambridge Center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710386/suppl/GSM710386_08_HMLE-msp3_b.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM710nnn/GSM710386/suppl/GSM710386_08_HMLE-msp3_b.CHP.gz
Sample_series_id	GSE28681
Sample_data_row_count	54675

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