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Sample GSM3976573 Query DataSets for GSM3976573
Status Public on May 22, 2020
Title Th17(23)_Control RNA-seq rep1
Sample type SRA
 
Source name TH17(23) cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Th17(23)
genotype: wildtype
Growth protocol Naïve CD4+ T cells were isolated from lymph nodes or spleen of mice using a CD4+ CD62L+ T cell isolation kit II (Miltenyi Biotec) according to the manufacturer’s instruction. Naïve CD4+ T cells were stimulated with plate-bound anti-CD3ε mAb (5 µg/ml) in the presence of anti-CD28 mAb (2 µg/ml) in a 48-well plate under neutral conditions (10 µg/ml anti–IL-4 mAb and 10 µg/ml anti–IFN-γ mAb), IL-6 conditions (10 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (23) conditions (20 ng/ml IL-6, 20 ng/ml IL-1β, 20 ng/ml IL-23, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb).
Extracted molecule total RNA
Extraction protocol Naive CD4+ T cells from control and miR-22-/- mice were differentiated under pathogenic TH17 (23) differentiation condition. Total RNA was prepared from these cells using Trizol reagent (Invitrogen). RNA-seq libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina). For GFP+ TH17 cells sorted from in vivo suspensions, 50,000 cells were resuspended in 700 ul Trizol reagent, total RNA was prepared by miRNeasy Micro Kit (Qiagen), RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (clontech). Sequencing was performed on an Illumina HiSeq X Ten System in a 150 bp/150 bp Paired end mode.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using CASAVA version 1.4
RNA-seq reads were mapped to mm10 with refGene annotation downloaded from UCSC Genome Browser using TopHat2 v2.1.0. Gene expression level were counted by htseq-count 0.11.0. Differential expressed genes were called by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text file included the raw reads count for each gene from RNA-seq sample.
 
Submission date Jul 25, 2019
Last update date May 22, 2020
Contact name Zhijun Han
E-mail(s) hangeneral@126.com
Organization name Southern University of Science and Technology
Street address No 1088,xueyuan Rd., Nanshan District
City Shenzhen
State/province Guangdong
ZIP/Postal code 518055
Country China
 
Platform ID GPL21273
Series (1)
GSE134895 The microRNA miR-22 represses T helper 17 cell pathogenicity by targeting PTEN-regulated pathways
Relations
BioSample SAMN12365018
SRA SRX6592078

Supplementary file Size Download File type/resource
GSM3976573_C1.readscount.txt.gz 98.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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