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Sample GSM2071733 Query DataSets for GSM2071733
Status Public on Jun 21, 2016
Title Th17 KO duplicate 1
Sample type SRA
Source name Th17 KO
Organism Mus musculus
Characteristics strain background: C57BL/6J
genotype/variation: miR-183C-/-
cell type: Th17 T cell
Growth protocol Control vector- or miR-96-overexpressing T cells and miR-183C+/+ or miR-183C-/- T cells were cultured under the Th17(23) condition and were harvested on day 4-5. Cell sorting was performed using a FACSAria cell sorter to obtain GFP-positive cells. Total RNA was extracted using the TRIzol reagent, enriched for polyA-containing RNAs and submitted to RNA-Seq.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using Trizol reagent.
RNAseq libraries were prepared using 500ng - 1.0 ug total RNA with the polyA selection module of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description F; Not Transduced
Data processing Basecalls performed using Illumina bcl2fastq/
Reads were aligned to Pre-built STAR 2.3.0 indexed Mouse genome, M. musculus UCSC mm10,
Generation of gene counts was performed using Partek® software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.
These data were filtered to exclude transcripts for which the maximum number of reads for all samples was <40 reads.
The mRNA-Seq data was analyzed using R Bioconductor package edgeR [Robinson et al., 2010], using the traditional GLM approach.
The results are first filtered with False Discovery Rate (FDR) >0.15 and then by log Counts Per Million (log2(CPM)) > 4.0.
Genome_build: mm10
Supplementary_files_format_and_content: microsoft excel,RefSeq mRNAs, gene read count.
Submission date Feb 25, 2016
Last update date May 15, 2019
Contact name Changchun Xiao
Phone (858) 784-7640
Organization name The Scripps Research Institute
Department Immunology & Microbial Science
Lab Changchun Xiao Lab
Street address 10550 North Torrey Pines Road
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
Platform ID GPL16417
Series (1)
GSE78505 Regulation of Th17 cell pathogenic function by miR-183/96/182
BioSample SAMN04516092
SRA SRX1600164

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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