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Sample GSM3348217 Query DataSets for GSM3348217
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).
 
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.
 
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

Supplementary file Size Download File type/resource
GSM3348217_EV_nonTFH_1.txt.gz 163.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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