Search results for the GEO ID: GSE42363  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1038341 | GPL570 |
|
ESO-837
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 58
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1b
pathological n: 0
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.05
non-silent mutation rate per mb (wes): 3.49
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038341
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038341/suppl/GSM1038341_4874.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038342 | GPL570 |
|
ESO-838
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 81
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1b
pathological n: 0
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.12
non-silent mutation rate per mb (wes): 3.93
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038342
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038342/suppl/GSM1038342_4875.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038343 | GPL570 |
|
ESO-874
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 72
ethnicity: Caucasian
location: esophagus
tumor grade: poorly
barrett's associated: yes
pathological t: T3
pathological n: 2
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.07
non-silent mutation rate per mb (wes): 2.99
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038343
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038343/suppl/GSM1038343_4886.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038344 | GPL570 |
|
ESO-913
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: female
age: 64
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: no
pathological t: T3
pathological n: 1
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.09
non-silent mutation rate per mb (wes): 2.86
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038344
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038344/suppl/GSM1038344_4892.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038345 | GPL570 |
|
ESO-1060
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 78
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1b
pathological n: 0
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.09
non-silent mutation rate per mb (wes): 4.19
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038345
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038345/suppl/GSM1038345_4915.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038346 | GPL570 |
|
ESO-130
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 76
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T2
pathological n: 0
clinical m: 0
smoking status: yes-former
pack years: 10
fraction of ap*a mutations: 0.06
non-silent mutation rate per mb (wes): 2.67
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038346
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038346/suppl/GSM1038346_1448.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038347 | GPL570 |
|
ESO-582
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 53
ethnicity: Caucasian
location: esophagus
tumor grade: poorly
barrett's associated: no
pathological t: T3
pathological n: 3
clinical m: 0
smoking status: yes- current
pack years: 40
fraction of ap*a mutations: 0.15
non-silent mutation rate per mb (wes): 2.98
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038347
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038347/suppl/GSM1038347_MS1077A.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038348 | GPL570 |
|
ESO-601
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 76
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1b
pathological n: 2
clinical m: 0
smoking status: yes-former
pack years: 20
fraction of ap*a mutations: 0.03
non-silent mutation rate per mb (wes): 3.5
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038348
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038348/suppl/GSM1038348_MS1079.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038349 | GPL570 |
|
ESO-682
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 59
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1b
pathological n: 0
clinical m: 0
smoking status: yes-current
pack years: 12
fraction of ap*a mutations: 0.11
non-silent mutation rate per mb (wes): 3.79
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038349
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038349/suppl/GSM1038349_MS1091.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038350 | GPL570 |
|
ESO-718
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 57
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T3
pathological n: 2
clinical m: 0
smoking status: yes-former
pack years: 20
fraction of ap*a mutations: 0.02
non-silent mutation rate per mb (wes): 2.64
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038350
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038350/suppl/GSM1038350_MS1098.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038351 | GPL570 |
|
ESO-721
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: female
age: 68
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1b
pathological n: 0
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.06
non-silent mutation rate per mb (wes): 8.35
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038351
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038351/suppl/GSM1038351_MS1100.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038352 | GPL570 |
|
ESO-774
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 54
ethnicity: Caucasian
location: esophagus
tumor grade: poorly
barrett's associated: no
pathological t: T3
pathological n: 3
clinical m: 0
smoking status: yes-former
pack years: 7
fraction of ap*a mutations: NA
non-silent mutation rate per mb (wes): NA
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038352
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038352/suppl/GSM1038352_MS1104.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038353 | GPL570 |
|
ESO-327
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 57
ethnicity: Caucasian
location: esophagus
tumor grade: poorly
barrett's associated: no
pathological t: T3
pathological n: 3
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.30
non-silent mutation rate per mb (wes): 4.42
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038353
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038353/suppl/GSM1038353_MS316.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
GSM1038354 | GPL570 |
|
ESO-409
|
esophageal adenocarcinoma (EAC) primary tumor
|
tissue type: Tumor
gender: male
age: 45
ethnicity: Caucasian
location: esophagus
tumor grade: moderately
barrett's associated: yes
pathological t: T1a
pathological n: 1
clinical m: 0
smoking status: no
pack years: 0
fraction of ap*a mutations: 0.08
non-silent mutation rate per mb (wes): 2.8
|
gene expression data from individual esophageal adenocarcinoma
|
| Sample_geo_accession | GSM1038354
| | Sample_status | Public on Feb 11 2013
| | Sample_submission_date | Nov 16 2012
| | Sample_last_update_date | Feb 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No radiation or chemotherapy
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)
| | Sample_hyb_protocol | Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.
| | Sample_scan_protocol | Processed microarrays were scanned using the GeneChip Scanner 7G.
| | Sample_data_processing | Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shouyong,,Peng
| | Sample_contact_email | shouyongpeng@gmail.com
| | Sample_contact_laboratory | Bass
| | Sample_contact_department | Medical Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 450 Brookline Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02215
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1038nnn/GSM1038354/suppl/GSM1038354_MS327.CEL.gz
| | Sample_series_id | GSE42363
| | Sample_data_row_count | 54675
| | |
|
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