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Sample GSM4055571 Query DataSets for GSM4055571
Status Public on Jun 01, 2020
Title RNA_ko-Tfh_2
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
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
BioSample SAMN12662962
SRA SRX6784718

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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