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Sample GSM1979029 Query DataSets for GSM1979029
Status Public on Jul 31, 2016
Title CXCR5+P14 #1
Sample type SRA
 
Source name splenic CD8+ T cells
Organism Mus musculus
Characteristics infection: Infected
cxcr5 expression: CXCR5+
activation: Activated CD44+
Extracted molecule polyA RNA
Extraction protocol Spleens were collected from infected mice to prepare single cell suspension. Target cells of interest were then sorted using flow cytometry and RNA was extracted using RNAeasy Kit from Qiagen.
PolyA RNA seq libraries prepared using Ilumina Stranded Sample prep, Protocol 15031047 RevD Sept 2012.
c-bot clustering using 12pM of library pool. Illumina Protocol 15006165 Rev K Oct 2012.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description X5plus-1
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed with Trimmomatic-0.32 using a leading and trailling quality cutoff of 24.
Trim_galore using a stringency of 3 to trim illumina adaptors.
The reads were mapped to the mm10 reference genome using STAR.
Reads were assigned to transcripts using HTSeq version 0.6.0 using the default setting.
Genome_build: Mus Musculus.GRCm38.75.
Supplementary_files_format_and_content: dyu_counts.txt
 
Submission date Dec 22, 2015
Last update date May 15, 2019
Contact name Yew Ann Leong
E-mail(s) yew.leong@monash.edu
Phone 03 9902 4675
Organization name Monash University
Department BIochemistry
Lab Immunomodulation Laboratory
Street address Wellington Road
City Clayton
State/province Victoria
ZIP/Postal code 3800
Country Australia
 
Platform ID GPL18480
Series (1)
GSE76279 CXCR5+ Follicular Cytotoxic T cells Control Viral Infection in B Cell follicles
Relations
BioSample SAMN04362873
SRA SRX1497698

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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