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Sample GSM1477264 Query DataSets for GSM1477264
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™.
 
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
 
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

Supplementary file Size Download File type/resource
GSM1477264_E35_Th9+TLA1_rep2.txt.gz 109.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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