|
| Status |
Public on Aug 30, 2016 |
| Title |
WT.Treg_RNAseq.4 |
| Sample type |
SRA |
| |
|
| Source name |
T-reg cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: WildType
mouse group: 2
strain: C57BL/6J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
Libraries were prepared with Illumina TruSeq Stranded mRNA sample kits using indexed adaptors (Illumina).
Pooled libraries were subjected to 75 bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Targeted sequencing depth was 30 million paired-end reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Mouse Group 2; Wild Type Treg Cells
|
| Data processing |
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
RNA sequencing reads were mapped with the TopHat 2 aligner using the default parameters to the UCSC mm10 mouse reference genome.
Reads were examined for quality control and quantified using FeatureCounts.
Raw counts were normalized taking into account library sizes, filtering out genes with ~0 expression (remaining gene, n=13700), and applying the variance-stabilizing transformation using the DESeq2 software package.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and normalized (varriance stabilized) text files as csv.
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey C Rathmell |
| E-mail(s) |
jeff.rathmell@vanderbilt.edu
|
| Organization name |
Vanderbilt University Medical Center
|
| Street address |
1161 21st Avenue South, A-5301 MCN
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232-2363 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE84919 |
Gene expression of Glut1 transgenic and control iTreg |
|
| Relations |
| BioSample |
SAMN05449635 |
| SRA |
SRX1981241 |
