|
Status |
Public on Jan 08, 2019 |
Title |
Th9+TLA1 rep2 |
Sample type |
SRA |
|
|
Source name |
T cell, Th9+TLA1 condition
|
Organism |
Mus musculus |
Characteristics |
cell type: T cell treatment: Th9+TLA1 condition
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from T cells using RNeasy kits (Qiagen, Valencia, CA) according to the manufacturer’s protocol Clontech’s SMARTer® Ultra™ Low Input RNA Kit for Sequencing v3 was employed to generate double-stranded cDNA libraries from 1.5 to 2.5 ng total RNA from each sample per manufacturer’s recommendations. Double-stranded cDNA libraries were individually fragmented and ligated with Ion Torrent Ion Xpress™ Barcode Adapters using Ion Xpress™ Plus Fragment Library Kit with limited modifications including size-selected final libraries with a double bead clean-up and ½ volume of Ion Adapters. RNA-Seq libraries were assessed for concentration and length using Invitrogen’s Qubit® dsDNA HS Assay Kit (Carlsbad, CA) and Agilent High Sensitivity DNA Kit respectively (Carlsbad, CA). Samples were multiplexed to obtain >10 million (11-15 million) reads each for sequencing. The pooled libraries were amplified onto Ion Sphere™ and sequenced using the Ion PI™ Sequencing 200 Kit v2, Ion Torrent™.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Ion Torrent Proton |
|
|
Data processing |
Raw reads were filtered and trimmed by FASTX toolkit Gene read counts were generated using HTSeq version 0.5.4 and then counts per million (CPM) were calculated by edgeR in Bioconductor. Genome_build: mm10 Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample
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|
|
Submission date |
Aug 12, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Jie Tang |
E-mail(s) |
jie.tang@cshs.org
|
Organization name |
Cedars Sinai Medical Center
|
Street address |
8700 Beverly Blvd
|
City |
Los Angeles |
ZIP/Postal code |
90048 |
Country |
USA |
|
|
Platform ID |
GPL18635 |
Series (1) |
GSE60362 |
TL1A signaling enhances the differentiation of TH9 cells and TH9-driven mucosal pathologies via BATF and BATF3 signaling pathways |
|
Relations |
BioSample |
SAMN02983289 |
SRA |
SRX675993 |