|
Status |
Public on Feb 11, 2019 |
Title |
EV_nonTFH_1 |
Sample type |
SRA |
|
|
Source name |
Isolated from lymph nodes 6 days after transfer and immunization
|
Organism |
Mus musculus |
Characteristics |
cell type: Antigen-specific non-Tfh cells transduction: control strain (mouse origin): C57BL/6 tissue: lymph node
|
Growth protocol |
T cells from Smarta TCR-transgenic mice crossed to CreERT2 mice were retrovirally transduced with an inducible Bach2 expression vector or an empty control vector and transferred into C57BL/6 recipients. Five days after s.c. immunization with nitrophenol and GP61-80 coupled to mouse serum albumin, ectopic Bach2 expression was induced by i.p. injection of tamoxifen. After 18 hours, transgenic T cells were isolated from pooled inguinal lymph nodes.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was purified with RNeasy Micro Kit (Qiagen) 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). For library preparation, the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) was used in combination with the Nextera XT library preparation kit (Illumina) according to the manufacturer's instructions. Paired-end sequencing with 2x75 nucleotides was performed on a NextSeq500 (Illumina).
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Antigen-specific non-Tfh cells transduced with a empty control vector
|
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 featureCounts. Genome_build: mm10 Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.
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|
|
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) |
GSE118822 |
Transcriptome analysis of antigen-specific T follicular helper (Tfh) and non-Tfh cells after Bach2 overexpression |
|
Relations |
BioSample |
SAMN09867728 |
SRA |
SRX4582005 |