|
| Status |
Public on Jan 01, 2018 |
| Title |
A9800_CD8_STAT1 Transgenic_90' media |
| Sample type |
SRA |
| |
|
| Source name |
sorted naive CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: STAT1 Transgenic
stimulus: 90' media
strain: C57BL/6
|
| Treatment protocol |
Sorted cell populations were spun down, adjusted at a concentration of 2x10^6 cells/ml prior to resting overnight for subsequent in vitro stimulation for 90 minutes at 37°C and 5% CO2 in presence or not of rmIL-7 (10 ng/ml) or rmIFN-γ (10 ng/ml; Peprotech).
|
| Growth protocol |
CD4+ and CD8+ naïve T cells from LNs of STAT1 Tg (n=4 and 5 respectively) and WT littermate (n=5 and 6 respectively) mice were sorted on a BD FACS Aria based on surface staining of CD8- CD4+ CD44low CD62L+ and CD8+ CD4- CD44low CD62L+ cell populations respectively. A mix of anti-B220, anti-CD49d (clone DX5; BioLegend),anti-Ter119 (clone TER-119; BioLegend), anti-MHC-II (clone M5/114.15.2; eBioscience) and anti-Gr-1 (clone RB6-8C5; BioLegend) was used in PE as a dump channel.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The cells were then washed once with PBS before being resuspended in TRIzol (Invitrogen) and stored at −80°C.
Illumina TrueSeq Stranded mRNA Library Prep kit from an input of 500 ng total RNA ("90-minute stimulation" samples) Illumina True-seq non-stranded mRNA ("overnight stimulation" samples)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A9800
|
| Data processing |
Adapter Trimmed reads were aligned to mouse genome version GRCm38 and mapped to ensemble gene features (v38.80, current June 2015) using Genomics Workbench software (CLC bio, version 8.0.2). Reads matching (10 or fewer) equally high scoring locations were assigned randomly.
Complete read-pairs mapping to specific (10 or fewer) exon locations were counted, Reads matching (10 or fewer) equally high scoring locations were assigned randomly.
Using JMP/Genomics software (SAS Institute), raw counts were inflated log-transformed and then normalized by upper quartile scaling
Genome_build: GRCm38
Supplementary_files_format_and_content: per-gene expression as log2(fragment count +1), where fragment count=total exon reads, normalization by Upper Quartile Scaling. Sample s17 filtered out from dataset due to low signal.
|
| |
|
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Timothy G Myers |
| E-mail(s) |
tgm@nih.gov
|
| Organization name |
National Institute of Allergy and Infectious Diseases
|
| Department |
Research Technologies Branch
|
| Lab |
Genomic Technologies Section
|
| Street address |
50 South Drive, Room 5509
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-8005 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE106575 |
IL-7-dependent STAT1 activation limits homeostatic CD4+ T cell expansion |
|
| Relations |
| BioSample |
SAMN07981650 |
| SRA |
SRX3367223 |
