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Sample GSM5945858 Query DataSets for GSM5945858
Status Public on Mar 01, 2024
Title Seq02_Th1_5
Sample type SRA
 
Source name activated murine CD4 T cells in vitro
Organism Mus musculus
Characteristics cell type: CD4 T cell
genotype: B6.Cg-Ifngtm3.1Lky-Il17atm1.1Lky
condition: Th1
Treatment protocol The cell culture are activated with plate-bound anti-CD3 and anti-CD28 and differentiated in the indicated conditions
Growth protocol Isolated naive CD4 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 Maxwell RSC miRNA Tissue Kit (Promega) and purified using Agencourt RNAClean XP Beads (Beckman Coulter)
Libraries were generated with the SENSE mRNA-Seq Lib Prep Kit V2 (Lexogen) using 100 ng RNA as input and with half of the volume as described in the manual. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
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
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts
 
Submission date Mar 10, 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 GPL18480
Series (1)
GSE198374 TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq02, bulk-RNAseq)
Relations
BioSample SAMN26565348
SRA SRX14430740

Supplementary file Size Download File type/resource
GSM5945858_Seq02_Th1_5.txt.gz 111.6 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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