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Series GSE85466 Query DataSets for GSE85466
Status Public on Sep 28, 2016
Title Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [SNP]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and super-enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic profiles of primary tumors, normal tissues, and cell lines
 
Overall design Genomic DNA extracted from gastric tumors and matched gastric non-malignant (normal) tissues was hybridized on Affymetrix SNP6 genotyping arrays. Normal samples (n=98) from this accession and 25 samples from GSE31168 were used to construct reference models by Affymetrix Genotyping Console 4.2.

Five samples from GSE36138 were also reanalyzed in this study.

Please note that a collective of normal SNP6 profiles were used to construct a reference model, which was used to normalise the cancer profiles. The copy number changes in the cancer profiles were then detected. The descriptions field contains details about each normal SNP6 profile that used for building the reference model for specified cancer profiles and corresponding processed file name.

The 'readme_re-analysis.txt' contains the details about the re-analyzed samples (e.g. sample characteristics, sample-to-file association etc.).
 
Contributor(s) Qamra A, Fong OW, Tan P
Citation(s) 27677335
Submission date Aug 11, 2016
Last update date Nov 27, 2018
Contact name Aditi Qamra
E-mail(s) qamraa99@gis.a-star.edu.sg
Organization name GIS
Street address 60 Biopolis Street, Genome, #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (19)
GSM2267426 FU97 [SNP]
GSM2267429 NCC-59 [SNP]
GSM2267433 YCC-21 [SNP]
This SubSeries is part of SuperSeries:
GSE85467 Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity
Relations
Reanalysis of GSM770076
Reanalysis of GSM770551
Reanalysis of GSM770558
Reanalysis of GSM770592
Reanalysis of GSM770928
Reanalysis of GSM770987
Reanalysis of GSM770999
Reanalysis of GSM771003
Reanalysis of GSM771004
Reanalysis of GSM771006
Reanalysis of GSM771007
Reanalysis of GSM771009
Reanalysis of GSM771038
Reanalysis of GSM771047
Reanalysis of GSM771127
Reanalysis of GSM772550
Reanalysis of GSM771097
Reanalysis of GSM771142
Reanalysis of GSM771051
Reanalysis of GSM771115
Reanalysis of GSM771133
Reanalysis of GSM771124
Reanalysis of GSM771116
Reanalysis of GSM771109
Reanalysis of GSM772540
Reanalysis of GSM888273
Reanalysis of GSM888402
Reanalysis of GSM888554
Reanalysis of GSM888613
Reanalysis of GSM888695
BioProject PRJNA338609

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE85466_RAW.tar 569.2 Mb (http)(custom) TAR (of BED, CEL)
GSE85466_re-analysis_KATO3_cna.bed.gz 1.2 Kb (ftp)(http) BED
GSE85466_re-analysis_MKN7_cna.bed.gz 2.3 Kb (ftp)(http) BED
GSE85466_re-analysis_OCUM1_cna.bed.gz 914 b (ftp)(http) BED
GSE85466_re-analysis_P2000085_cna.bed.gz 510 b (ftp)(http) BED
GSE85466_re-analysis_P2000721_cna.bed.gz 1.1 Kb (ftp)(http) BED
GSE85466_re-analysis_P2000986_cna.bed.gz 684 b (ftp)(http) BED
GSE85466_re-analysis_P20021007_cna.bed.gz 792 b (ftp)(http) BED
GSE85466_re-analysis_P76629543_cna.bed.gz 1.7 Kb (ftp)(http) BED
GSE85466_re-analysis_P980097_cna.bed.gz 553 b (ftp)(http) BED
GSE85466_re-analysis_P980319_cna.bed.gz 650 b (ftp)(http) BED
GSE85466_re-analysis_P980401_cna.bed.gz 510 b (ftp)(http) BED
GSE85466_re-analysis_P980417_cna.bed.gz 784 b (ftp)(http) BED
GSE85466_re-analysis_P980436_cna.bed.gz 670 b (ftp)(http) BED
GSE85466_re-analysis_P980437_cna.bed.gz 360 b (ftp)(http) BED
GSE85466_re-analysis_P980447_cna.bed.gz 743 b (ftp)(http) BED
GSE85466_re-analysis_P990275_cna.bed.gz 955 b (ftp)(http) BED
GSE85466_re-analysis_P990489_cna.bed.gz 546 b (ftp)(http) BED
GSE85466_re-analysis_RERF-GC-1B_cna.bed.gz 1.6 Kb (ftp)(http) BED
GSE85466_re-analysis_SNU16_cna.bed.gz 1.8 Kb (ftp)(http) BED
GSE85466_readme_re-analysis.txt 15.3 Kb (ftp)(http) TXT
Processed data provided as supplementary file

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