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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.
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|
|
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
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|
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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 |