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Status |
Public on Feb 15, 2018 |
Title |
Junb KO, Th17 cell, replicate 2 |
Sample type |
SRA |
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Source name |
Junb KO mouse, Th17 cell
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Organism |
Mus musculus |
Characteristics |
cell type: Th17 cell strain: C57BL/6J genotype: Junb-/-
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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.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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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
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Organization name |
Kyushu University
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Street address |
744 Motooka Nishi-Ku
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City |
Fukuoka |
ZIP/Postal code |
819-0395 |
Country |
Japan |
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Platform ID |
GPL17021 |
Series (1) |
GSE98242 |
The AP-1 Transcription Factor JunB Is Required for Th17 Cell Differentiation |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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