|
| Status |
Public on Jun 21, 2016 |
| Title |
Th17 WT duplicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Th17 WT
|
| 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 NextSeq 500 |
| |
|
| Description |
E; Not Transduced
|
| 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 |
SAMN04516091 |
| SRA |
SRX1600163 |
