|
| Status |
Public on Mar 01, 2024 |
| Title |
Seq01_Th1_5 |
| Sample type |
SRA |
| |
|
| Source name |
activated murine CD4 T cells in vitro
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD4 T cell
genotype: C57BL/6
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) |
| GSE198370 |
TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq01, bulk-RNAseq) |
|
| Relations |
| BioSample |
SAMN26565270 |
| SRA |
SRX14430690 |
