Search results for the GEO ID: GSE9574  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM241999 | GPL96 |
|
reduction mammoplasty patient 288
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 288
age-at-biopsy-years: 52
|
reduction mammoplasty histologically normal breast epithlieum patient 288
|
| Sample_geo_accession | GSM241999
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM241nnn/GSM241999/suppl/GSM241999.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242000 | GPL96 |
|
reduction mammoplasty patient 278
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 278
age-at-biopsy-years: 44
|
reduction mammoplasty histologically normal breast epithlieum patient 278
|
| Sample_geo_accession | GSM242000
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242000/suppl/GSM242000.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242001 | GPL96 |
|
reduction mammoplasty patient 309
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 309
age-at-biopsy-years: 49
|
reduction mammoplasty histologically normal breast epithlieum patient 309
|
| Sample_geo_accession | GSM242001
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242001/suppl/GSM242001.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242002 | GPL96 |
|
reduction mammoplasty patient 310
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 310
age-at-biopsy-years: 60
|
reduction mammoplasty histologically normal breast epithlieum patient 310
|
| Sample_geo_accession | GSM242002
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242002/suppl/GSM242002.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242003 | GPL96 |
|
reduction mammoplasty patient 314
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 314
age-at-biopsy-years: 49
|
reduction mammoplasty histologically normal breast epithlieum patient 314
|
| Sample_geo_accession | GSM242003
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242003/suppl/GSM242003.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242004 | GPL96 |
|
reduction mammoplasty patient 334
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 334
age-at-biopsy-years: 42
|
reduction mammoplasty histologically normal breast epithlieum patient 334
|
| Sample_geo_accession | GSM242004
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242004/suppl/GSM242004.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242005 | GPL96 |
|
reduction mammoplasty patient 340
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 340
age-at-biopsy-years: 41
|
reduction mammoplasty histologically normal breast epithlieum patient 340
|
| Sample_geo_accession | GSM242005
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242005/suppl/GSM242005.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242006 | GPL96 |
|
reduction mammoplasty patient 350
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 350
age-at-biopsy-years: 47
|
reduction mammoplasty histologically normal breast epithlieum patient 350
|
| Sample_geo_accession | GSM242006
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242006/suppl/GSM242006.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242007 | GPL96 |
|
reduction mammoplasty patient 357
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 357
age-at-biopsy-years: 49
|
reduction mammoplasty histologically normal breast epithlieum patient 357
|
| Sample_geo_accession | GSM242007
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242007/suppl/GSM242007.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242008 | GPL96 |
|
reduction mammoplasty patient 347
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 347
age-at-biopsy-years: 43
|
reduction mammoplasty histologically normal breast epithlieum patient 347
|
| Sample_geo_accession | GSM242008
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242008/suppl/GSM242008.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242009 | GPL96 |
|
reduction mammoplasty patient 352
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 352
age-at-biopsy-years: 41
|
reduction mammoplasty histologically normal breast epithlieum patient 352
|
| Sample_geo_accession | GSM242009
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242009/suppl/GSM242009.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242010 | GPL96 |
|
reduction mammoplasty patient 361
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 361
age-at-biopsy-years: 57
|
reduction mammoplasty histologically normal breast epithlieum patient 361
|
| Sample_geo_accession | GSM242010
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242010/suppl/GSM242010.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242011 | GPL96 |
|
reduction mammoplasty patient 328
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 328
age-at-biopsy-years: 39
|
reduction mammoplasty histologically normal breast epithlieum patient 328
|
| Sample_geo_accession | GSM242011
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242011/suppl/GSM242011.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242012 | GPL96 |
|
reduction mammoplasty patient 360
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 360
age-at-biopsy-years: 36
|
reduction mammoplasty histologically normal breast epithlieum patient 360
|
| Sample_geo_accession | GSM242012
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242012/suppl/GSM242012.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242013 | GPL96 |
|
reduction mammoplasty patient 368
|
breast epithelium from reduction mammoplasty
|
disease-state: normal (reduction mammoplasty)
tissue-type: breast epithlieum
patient-id: 368
age-at-biopsy-years: 49
|
reduction mammoplasty histologically normal breast epithlieum patient 368
|
| Sample_geo_accession | GSM242013
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242013/suppl/GSM242013.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242014 | GPL96 |
|
breast cancer patient 251
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 251
age-at-biopsy-years: 45
|
breast cancer histologically normal breast epithlieum patient 251
|
| Sample_geo_accession | GSM242014
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242014/suppl/GSM242014.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242015 | GPL96 |
|
breast cancer patient 318
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 318
age-at-biopsy-years: 38
|
breast cancer histologically normal breast epithlieum patient 318
|
| Sample_geo_accession | GSM242015
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242015/suppl/GSM242015.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242016 | GPL96 |
|
breast cancer patient 320
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 320
age-at-biopsy-years: 34
|
breast cancer histologically normal breast epithlieum patient 320
|
| Sample_geo_accession | GSM242016
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242016/suppl/GSM242016.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242017 | GPL96 |
|
breast cancer patient 359
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 359
age-at-biopsy-years: 48
|
breast cancer histologically normal breast epithlieum patient 359
|
| Sample_geo_accession | GSM242017
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242017/suppl/GSM242017.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242018 | GPL96 |
|
breast cancer patient 297B
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 297B
age-at-biopsy-years: 46
|
breast cancer histologically normal breast epithlieum patient 297B
|
| Sample_geo_accession | GSM242018
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242018/suppl/GSM242018.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242019 | GPL96 |
|
breast cancer patient 316
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 316
age-at-biopsy-years: 39
|
breast cancer histologically normal breast epithlieum patient 316
|
| Sample_geo_accession | GSM242019
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242019/suppl/GSM242019.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242020 | GPL96 |
|
breast cancer patient 304B
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 304B
age-at-biopsy-years: 49
|
breast cancer histologically normal breast epithlieum patient 304B
|
| Sample_geo_accession | GSM242020
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242020/suppl/GSM242020.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242021 | GPL96 |
|
breast cancer patient 351
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 351
age-at-biopsy-years: 35
|
breast cancer histologically normal breast epithlieum patient 351
|
| Sample_geo_accession | GSM242021
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242021/suppl/GSM242021.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242022 | GPL96 |
|
breast cancer patient 248
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 248
age-at-biopsy-years: 49
|
breast cancer histologically normal breast epithlieum patient 248
|
| Sample_geo_accession | GSM242022
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242022/suppl/GSM242022.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242023 | GPL96 |
|
breast cancer patient 226
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 226
age-at-biopsy-years: 61
|
breast cancer histologically normal breast epithlieum patient 226
|
| Sample_geo_accession | GSM242023
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242023/suppl/GSM242023.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242024 | GPL96 |
|
breast cancer patient 258
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 258
age-at-biopsy-years: 65
|
breast cancer histologically normal breast epithlieum patient 258
|
| Sample_geo_accession | GSM242024
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242024/suppl/GSM242024.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242025 | GPL96 |
|
breast cancer patient 274
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 274
age-at-biopsy-years: 49
|
breast cancer histologically normal breast epithlieum patient 274
|
| Sample_geo_accession | GSM242025
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242025/suppl/GSM242025.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
| | |
|
GSM242026 | GPL96 |
|
breast cancer patient 232
|
breast epithelium adjacent to tumor
|
disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 232
age-at-biopsy-years: 59
|
breast cancer histologically normal breast epithlieum patient 232
|
| Sample_geo_accession | GSM242026
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242026/suppl/GSM242026.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
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GSM242027 | GPL96 |
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breast cancer patient 237
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breast epithelium adjacent to tumor
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disease-state: breast cancer
tissue-type: breast epithlieum
patient-id: 237
age-at-biopsy-years: 55
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breast cancer histologically normal breast epithlieum patient 237
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| Sample_geo_accession | GSM242027
| | Sample_status | Public on Dec 10 2007
| | Sample_submission_date | Nov 09 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion. In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
| | Sample_hyb_protocol | For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
| | Sample_scan_protocol | The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing = MAS5.0, target intensity | 500
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marc,E.,Lenburg
| | Sample_contact_email | mlenburg@bu.edu
| | Sample_contact_phone | 617-414-1375
| | Sample_contact_fax | 617-414-1646
| | Sample_contact_department | Genetics and Genomics
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 715 Albany Street, E613B
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02130
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://gg.bu.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM242nnn/GSM242027/suppl/GSM242027.CEL.gz
| | Sample_series_id | GSE9574
| | Sample_data_row_count | 22283
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