|
Status |
Public on Jun 21, 2016 |
Title |
Th17 Control duplicate 1 |
Sample type |
SRA |
|
|
Source name |
Th17 Control
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6J genotype/variation: control vector-expressing 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 NextSeq 500 |
|
|
Description |
A; Transduced with control vector
|
Data processing |
Basecalls performed using Illumina bcl2fastq/2.16.0.10 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 |
E-mail(s) |
cxiao@scripps.edu
|
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 |
GPL19057 |
Series (1) |
GSE78505 |
Regulation of Th17 cell pathogenic function by miR-183/96/182 |
|
Relations |
BioSample |
SAMN04516087 |
SRA |
SRX1600159 |