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Sample GSM1536043 Query DataSets for GSM1536043
Status Public on Nov 09, 2015
Title SOX15 shRNA biological rep1 (RNA-Seq)
Sample type SRA
Source name CPA cells
Organism Homo sapiens
Characteristics cell line: Barrett's esophagus cell line, CPA
genotype/variation: SOX15 depletion
Treatment protocol Cells were infected with non specific or SOX15 shRNA
Growth protocol Cells were harvested and frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
The TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Sample name: SOX15-2
processed data file: Differential_gene_exp.diff
Data processing base-calling: bcl2fastq, version for Illumina NextSeq 500 with default settings.
alignment: Starstatic, version 2.3.1 with default settings
normalized and differential expression: Cufflinks, version 2.0.2; settings: default; Cuffdiff was used with default settings.
Supplementary_files_format_and_content: [RNA-Seq] Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals. Data is also represented as differential expression table prepared using Cuffdiff with an FDR of 5%, which contains average normalized FPKM values for Control SC and Sox15 knockout samples, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
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
Platform ID GPL18573
Series (1)
GSE62909 SOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas
BioSample SAMN03159555
SRA SRX878127

Supplementary file Size Download File type/resource
GSM1536043_Sox15-2.genes.fpkm_tracking.gz 630.4 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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