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Sample GSM4055570 Query DataSets for GSM4055570
Status Public on Jun 01, 2020
Title RNA_ko-Tfh_1
Sample type SRA
 
Source name CD4positiveCD45.1positiveCXCR5hiPD1hi
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
genotype: Ly5.1
Treatment protocol WT OT-II or Tox2-/- SMARTA mice were transferred into Ly5.1 mice, followed by LCMV infection.
Extracted molecule total RNA
Extraction protocol Two populations from Transferred ly5.1 mice were isolated by cell sorting (Tfh: CD4+CD45.1+CXCR5hiPD-1hi, nonTfh: CD4+CD45.1+CXCR5-PD-1- ).
Total RNA were extracted using Trizol(Thermo), and sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were cleaned for trimming adaptor sequence, low-quality sequence (Q<20) from the 3' end, and filtering the reads with the length less than 20.
Cleaned reads were then quantified with the indexed mouse transcriptome Mus_musculus.GRCm38.cdna using the salmon program
The Salmon-generated quantification files were read in by DESeq2 package in R and generated normalized transcript quantification by "mean-ratio method".
Genome_build: ensembl reference transcriptome mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: tab-delimited text files of raw transcript quantification files(from salmon program) and normalized files (normalized by mean-ratio method)
 
Submission date Aug 30, 2019
Last update date Jun 01, 2020
Contact name Jinyi Tang
E-mail(s) taotao11011011@163.com
Phone 17721241521
Organization name IPS
Lab Wang Haikun
Street address Yueyang road 320
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL21273
Series (1)
GSE136694 Transcription Factor Tox2 is required for Follicular Helper T Cells differentiation
Relations
BioSample SAMN12662963
SRA SRX6784717

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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