NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2589771 Query DataSets for GSM2589771
Status Public on Feb 15, 2018
Title Junb KO, Th17 cell, replicate 2
Sample type SRA
 
Source name Junb KO mouse, Th17 cell
Organism Mus musculus
Characteristics cell type: Th17 cell
strain: C57BL/6J
genotype: Junb-/-
Treatment protocol Naive CD4+ T cells were prepared from the spleen and lymph nodes of 6–9 week old mice by magnetic sorting using DynabeadsⓇ Mouse CD4 (L3T4, Invitrogen) and DETACHaBEADⓇ Mouse CD4 (Invitrogen), as described previously (Tanaka et al., 2007). The CD4+ T cells were activated for 3 days via TCR with plate-bound 5 ug/ml of an anti-CD3 antibody (145-2C11, BioLegend) and soluble 2.5 ug/ml of an anti-CD28 antibody (35.71, BioLegend) under the following differentiation conditions: 10 ug/ml of an anti-IFN- antibody (XMG 1.2, BioLegend) and 10 ug/ml of an anti-IL-4 antibody (11B11, BioLegend) for Th0; 10 ug/ml of the anti-IFN- antibody, 10 ug/ml of the anti-IL-4 antibody, 40 ng/ml of mouse IL-6 (Peprotech), and 4 ng/ml of human TGF-1 (R&D) for Th17; 10 ug/ml of the anti-IL-4 antibody and 40 ng/ml of mouse IL-12 p70 (BioLegend) for Th1; 10 ug/ml of the anti-IFN- antibody and 40 ng/ml of mouse IL-4 (Peprotech) for Th2; 10 ug/ml of the anti-IFN- antibody, 10 ug/ml of the anti-IL-4 antibody, 4 ng/ml of human TGF-1 for Treg.
Growth protocol Junbf/f mice were generated according to the standard technique (Gomi et al., 1995; Endo et al., 1995), and crossed with Meox2Cre/+ mice (Tallquist et al., 2000) (Jackson laboratory) for generation of Junb-deficient (Junbf/f;Meox2Cre/+) mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extacted using TRIsure (BIOLINE, London, UK) and treated with Rnase-free DNase (Promega, Madison).
Two and a half micrograms of total RNA was subjected to ribosomal RNA depletion using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre) followed by RNA-seq library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Each library was quantified using Kapa Library Quantitation Kit (Kappa) and sequenced on Illumina HiSeq2500 to generate 101-bp paired-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads were trimmed for adapter sequences and low-quality reads using Trimmomatic version 0.32 (Bolger et al., 2014) and were then aligned to the mouse reference genome mm9 using TopHat version 2.0.13 (Kim et al. 2013). For each gene, reads were counted using featureCounts (Liao et al., 2014). Finally, edgeR was used to normalize read count by the TMM procedure and perform differential expression analyses (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
 
Submission date Apr 26, 2017
Last update date May 15, 2019
Contact name Hiromitsu Araki
E-mail(s) araki.hiromitsu.596@m.kyushu-u.ac.jp
Organization name Kyushu University
Street address 744 Motooka Nishi-Ku
City Fukuoka
ZIP/Postal code 819-0395
Country Japan
 
Platform ID GPL17021
Series (1)
GSE98242 The AP-1 Transcription Factor JunB Is Required for Th17 Cell Differentiation
Relations
BioSample SAMN06835242
SRA SRX2765950

Supplementary file Size Download File type/resource
GSM2589771_KO_Th17_rep2.txt.gz 1.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap