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Sample GSM5917189 Query DataSets for GSM5917189
Status Public on Mar 01, 2024
Title Seq03_Tfh2_4e4_2
Sample type SRA
 
Source name activated murine CD4 T cells in vitro
Organism Mus musculus
Characteristics cell type: CD4 T cell
strain: C57BL/6
condition: Tfh2_4e4
Treatment protocol The cells were activated with plate-bound anti-CD3 and anti-CD28 and differentiated in the indicated conditions
Growth protocol Isolated naive CD4 T cells were cultured in cRPMI for 3.5 days
Extracted molecule total RNA
Extraction protocol Cells were stained for flow cytometry and and sorted directly into Trizol LS. RNA was isolated using Chloroform-Extraction followed by a RNA-purification via spin-columns.
Libraries were generated according to manufacturer´s guidelines with the 3‘ mRNA-Seq Library Prep Kit FWD with Unique Dual Indices (Lexogen) using 50 ng total RNA as input.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Seq03_DE90NGSUKBR116699
Data processing Fastq files were demultiplexes with Multi Demultiplex (Galaxy Version 1.0) using Illumina Index file
All raw fastq data were mapped to the mouse genome (mm10) using STAR 2.7.2b (Dobin et al., 2013)
Count matrices were generated using FeatureCount 1.6.4 (Liao et al., 2014) with the gene annotation file for mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts
 
Submission date Feb 24, 2022
Last update date Mar 01, 2024
Contact name Dirk Baumjohann
E-mail(s) dirk.baumjohann@uni-bonn.de
Organization name University Hospital Bonn
Department Medical Clinic III
Lab Baumjohann Lab
Street address Venusberg-Campus 1
City Bonn
State/province NRW
ZIP/Postal code 53127
Country Germany
 
Platform ID GPL24247
Series (1)
GSE197425 TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq03, bulk-RNAseq)
Relations
BioSample SAMN26236142
SRA SRX14283083

Supplementary file Size Download File type/resource
GSM5917189_Seq03_Tfh2_4e4_2.txt.gz 106.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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