|
| Status |
Public on Feb 11, 2019 |
| Title |
T53 TFH |
| Sample type |
SRA |
| |
|
| Source name |
Isolated from lymph nodes 8 days after transfer and immunization
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Antigen-specific Tfh cells
strain (mouse origin): C57BL/6
tissue: lymph node
|
| Growth protocol |
T cells from OT-II TCR-transgenic mice were transferred into C57BL/6 recipients, which were subsequently immunized s.c. with nitrophenol coupled to ovalbumin. Transgenic T cells were isolated from pooled inguinal lymph nodes on day 8 after immunization.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified with the Roche High Pure RNA Isolation Kit from FACS-sorted antigen-specific (Thy-1.1+) CD44hi CXCR5+ PD-1+ Tfh and CXCR5- PD-1- non-Tfh cells isolated from inguinal lymph nodes. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
The library was prepared using the TruSeq® Stranded Total RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions. Paired-end sequencing with 2x75 nucleotides was performed on a NextSeq500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.
|
| |
|
| Submission date |
Aug 21, 2018 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Pawel Durek |
| E-mail(s) |
pawel.durek@drfz.de
|
| Organization name |
Deutsches Rheuma-Forschungszentrum
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE118821 |
Transcriptome analysis of antigen-specific T follicular helper (Tfh) cells and non-Tfh cells |
|
| Relations |
| BioSample |
SAMN09867721 |
| SRA |
SRX4582026 |
