|
| Status |
Public on Nov 09, 2015 |
| Title |
Control 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: control
|
| 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: SC1
processed data file: Differential_gene_exp.diff
|
| Data processing |
base-calling: bcl2fastq, version 02.14.01.07 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.
Genome_build:hg19
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 |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN03159553 |
| SRA |
SRX878125 |
