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Series GSE62909 Query DataSets for GSE62909
Status Public on Nov 09, 2015
Title SOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We identified spatially restricted transcription factors and found SOX15 expression confined to stratified esophageal epithelium, with attenuation in Barrett's esophagus.
SOX15 binds esophagus-specific loci and its loss in human esophageal cells affected esophagus-specific transcripts
Overall design [RNA-Seq] Total RNA isolated from CPA control cells and CPA cells following SOX15 depletion, samples were prepared for sequencing using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions. 75 base pair single-end reads were sequenced on an Illumina NextSeq 500 instrument. The data include 2 independent biological replicates per genotype.
[ChIP-Seq] Examine SOX15-chromatin binding in CPA cells.
Contributor(s) Sulahian R, Chen J, Arany Z, Jadhav U, Peng S, Rustgi AK, Bass AJ, Srivastava A, Hornick JL, Shivdasani RA
Citation(s) 26516633
Submission date Oct 31, 2014
Last update date May 15, 2019
Contact name Ramesh Shivdasani
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Lab Shivdasani
Street address 450 Brookline Ave. Dana 720D
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM1536041 Control biological rep1 (RNA-Seq)
GSM1536042 Control biological rep2 (RNA-Seq)
GSM1536043 SOX15 shRNA biological rep1 (RNA-Seq)
BioProject PRJNA266111
SRA SRP049465

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

Supplementary file Size Download File type/resource
GSE62909_Differential_gene_exp.diff.gz 803.4 Kb (ftp)(http) DIFF
GSE62909_RAW.tar 297.4 Mb (http)(custom) TAR (of BED, FPKM_TRACKING, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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