Search results for the GEO ID: GSE6885  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM158659 | GPL570 |
|
BPE sample 1
|
Normal human mammary epithelial cells
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells
|
| Sample_geo_accession | GSM158659
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). These were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158659/suppl/GSM158659.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158660 | GPL570 |
|
BPE sample 2
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158660
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). These were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158660/suppl/GSM158660.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158661 | GPL570 |
|
BPE sample 3
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158661
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158661/suppl/GSM158661.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158662 | GPL570 |
|
BPE sample 4
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158662
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158662/suppl/GSM158662.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158663 | GPL570 |
|
BPE sample 5
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158663
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158663/suppl/GSM158663.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158664 | GPL570 |
|
BPLER sample 1
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158664
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158664/suppl/GSM158664.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158665 | GPL570 |
|
BPLER sample 2
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158665
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158665/suppl/GSM158665.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158666 | GPL570 |
|
BPLER sample 3
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158666
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158666/suppl/GSM158666.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158667 | GPL570 |
|
BPLER sample 4
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158667
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158667/suppl/GSM158667.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158668 | GPL570 |
|
BPLER sample 5
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158668
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158668/suppl/GSM158668.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158669 | GPL570 |
|
BPLER sample 6
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158669
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in WIT medium
| | Sample_growth_protocol_ch1 | in vitro cultured in WIT medium on Primaria plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158669/suppl/GSM158669.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158670 | GPL570 |
|
HME sample 1
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158670
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158670/suppl/GSM158670.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158671 | GPL570 |
|
HMLER sample 6
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158671
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
| | Sample_data_processing | was used to generate a cell intensity file (*.cel). Probe intensities were
| | Sample_data_processing | normalized and summarized using GCRMA (with default settings)
| | Sample_data_processing | with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158671/suppl/GSM158671.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158672 | GPL570 |
|
HME sample 3
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158672
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158672/suppl/GSM158672.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158673 | GPL570 |
|
HME sample 4
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158673
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158673/suppl/GSM158673.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158674 | GPL570 |
|
HME sample 2
|
Normal human mammary epithelial cells, hTERT-immortalized
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
Normal human mammary epithelial cells, hTERT-immortalized
|
| Sample_geo_accession | GSM158674
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | immortalized by hTERT in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158674/suppl/GSM158674.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158675 | GPL570 |
|
HMLER sample 1
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158675
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158675/suppl/GSM158675.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158676 | GPL570 |
|
HMLER sample 2
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158676
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158676/suppl/GSM158676.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158677 | GPL570 |
|
HMLER sample 3
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158677
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158677/suppl/GSM158677.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158678 | GPL570 |
|
HMLER sample 4
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158678
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158678/suppl/GSM158678.CEL.gz
| | Sample_series_id | GSE6885
| | Sample_data_row_count | 54675
| | |
|
GSM158679 | GPL570 |
|
HMLER sample 5
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
Gender: female
Age: premenopausal
Tissue: normal breast
Disease: none
|
BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)
|
| Sample_geo_accession | GSM158679
| | Sample_status | Public on Aug 15 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Aug 15 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Brigham and Women's Hospital
| | Sample_treatment_protocol_ch1 | transformed by SV40 - largeT/smallT + H-Ras in MEGM medium
| | Sample_growth_protocol_ch1 | in vitro cultured in MEGM medium on regular culture plates
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The standard protocols followed were per Affymetrix’s instructions
| | Sample_extract_protocol_ch1 | (Genechip Expression Analysis Technical Manual
| | Sample_extract_protocol_ch1 | 701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
| | Sample_extract_protocol_ch1 | instructions. The RNA pellet was resuspended in 100 ul
| | Sample_extract_protocol_ch1 | of RNAse free water. The RNeasy Clean-up kit (Qiagen,
| | Sample_extract_protocol_ch1 | Valencia, CA) was utilized per manufacturer’s instructions
| | Sample_extract_protocol_ch1 | resulting in 30 ul total RNA sample. The total RNA concentration
| | Sample_extract_protocol_ch1 | and 260/280 ratio was evaluated on a NanoDrop ND-
| | Sample_extract_protocol_ch1 | 1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
| | Sample_extract_protocol_ch1 | Rockland, DE). Only samples with a 260/280 ratio greater
| | Sample_extract_protocol_ch1 | than 1.9 were further processed. An aliquot of 1 ul from each
| | Sample_extract_protocol_ch1 | of the samples was diluted to be within the dynamic range of
| | Sample_extract_protocol_ch1 | the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
| | Sample_extract_protocol_ch1 | CA), with a target of 100 ng. The Nano Labchip protocol was
| | Sample_extract_protocol_ch1 | followed as per manufacturer’s instructions and was placed
| | Sample_extract_protocol_ch1 | on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
| | Sample_extract_protocol_ch1 | evaluation. Samples with the highest concentration, only 2
| | Sample_extract_protocol_ch1 | distinct 18 S and 28 S peaks, and no evidence of degradation
| | Sample_extract_protocol_ch1 | were further processed.
| | Sample_extract_protocol_ch1 | To obtain 15 µg of total RNA for first strand cDNA synthesis,
| | Sample_extract_protocol_ch1 | samples were sometimes combined and placed on a spinvacuum
| | Sample_extract_protocol_ch1 | to obtain the necessary concentration (1.66 µg/µl)
| | Sample_extract_protocol_ch1 | and volume (9µl). Six hundred units of SuperScript II reverse
| | Sample_extract_protocol_ch1 | transcriptase were used for the first strand cDNA synthesis
| | Sample_extract_protocol_ch1 | reaction.
| | Sample_extract_protocol_ch1 | The second strand DNA synthesis, the clean-up of
| | Sample_extract_protocol_ch1 | the double-stranded cDNA, the synthesis of the biotin-labeled
| | Sample_extract_protocol_ch1 | cRNA, and the clean-up of the biotin-labeled cRNA were
| | Sample_extract_protocol_ch1 | per Affymetrix instructions. The Genechip Sample Cleanup
| | Sample_extract_protocol_ch1 | module was used for the clean-up steps of the double stranded
| | Sample_extract_protocol_ch1 | cDNA and the biotin-labeled cRNA. Quantification
| | Sample_extract_protocol_ch1 | of the cRNA was evaluated on the NanoDrop. Samples were
| | Sample_extract_protocol_ch1 | used for hybridization only if 20 µg of cRNA were obtained
| | Sample_extract_protocol_ch1 | in an individual sample or by combining samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | As per Affymetrix instructions
| | Sample_hyb_protocol | Fragmentation, hybridization, washing, staining, and scanning
| | Sample_hyb_protocol | were done according to the Affymetrix protocol. Briefly,
| | Sample_hyb_protocol | reagent preparation included 12X MES stock (1.22 M MES,
| | Sample_hyb_protocol | 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization
| | Sample_hyb_protocol | buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%
| | Sample_hyb_protocol | Tween 20). The hybridization cocktail components and final
| | Sample_hyb_protocol | concentrations consisted of fragmented cDNA (.05 µg/µl),
| | Sample_hyb_protocol | control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization
| | Sample_hyb_protocol | controls bioB, bioC, bioD, and cre (1.5, 5, 25,
| | Sample_hyb_protocol | 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated
| | Sample_hyb_protocol | BSA (.5 mg/ml), 1X hybridization buffer with a final
| | Sample_hyb_protocol | volume of 300 µl. The GeneChip array was filled with 250 µl
| | Sample_hyb_protocol | of the hybridization cocktail and hybridized for 16 hours, rotated
| | Sample_hyb_protocol | at 60 RPM, and maintained at 45C.
| | Sample_hyb_protocol | Reagents prepared for washing and staining included a
| | Sample_hyb_protocol | nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent
| | Sample_hyb_protocol | wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween
| | Sample_hyb_protocol | 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],
| | Sample_hyb_protocol | 0.05% Tween 20). The wash procedure was carried out in
| | Sample_hyb_protocol | an Affymetrix Fluidics Station 400 controlled by Affymetrix
| | Sample_hyb_protocol | Microarray Suite 5.0 software resident on a personal computer.
| | Sample_hyb_protocol | The fluidics station first went through a priming step
| | Sample_hyb_protocol | and subsequently did the washing and staining by a software
| | Sample_hyb_protocol | protocol.
| | Sample_scan_protocol | The microarrays were scanned using the GeneArray scanner
| | Sample_scan_protocol | per manufacturer’s instructions (Affymetrix, Santa Clara,
| | Sample_scan_protocol | CA). The quality control algorithms for eliminating an array
| | Sample_scan_protocol | are based on recommendations in both the Affymetrix and
| | Sample_scan_protocol | dChip software packages.
| | Sample_data_processing | Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tan,A,Ince
| | Sample_contact_laboratory | Weinberg
| | Sample_contact_institute | Whitehead Institute
| | 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_contact_web_link | http://web.wi.mit.edu/weinberg/pub/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM158nnn/GSM158679/suppl/GSM158679.CEL.gz
| | Sample_series_id | GSE6885
| | 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: |
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