|
| Status |
Public on May 01, 2017 |
| Title |
C57BL6_TCR-activated |
| Sample type |
SRA |
| |
|
| Source name |
T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
genotype: wildtype
developmental stage: TCR-activated
cell type: T cells
|
| Treatment protocol |
Naïve or expanded T cells were stimulated with 10 μg/ml DMXAA (Invivogen) unless otherwise indicated; for experiments involving TCR activation, tissue culture plates were coated overnight with anti-CD3 and anti-CD28 antibodies (BD Bioscience; Biolegend) at 5 μg/ml.
|
| Growth protocol |
T cell purification and expansion: Naïve total CD3+, CD4+, and CD8+ T cells were isolated from mouse spleens and pLN using STEMCELL Technologies (Vancouver, BC) EasySep Mouse T cell isolation kits according to manufacturer’s instructions. Expanded T cells were prepared using Mouse T activator CD3/CD28 DynaBeads (ThermoFisher Scientific) in complete RPMI with 10% FBS and 50 U/ml recombinant IL-2. Cells were rested overnight in complete media without IL-2 before experiments.
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared according to manufacture's instructions
Library was prepared using Truseq pair-end Illumina kit. Briefly, 10-100 ng of total RNA was reconstituted in water, mixed with Ribosomal removal Buffer containing RNAClean XP beads, and depleted from rRNA. First strand was synthesized using RT, followed by a second strand synthesis, 3' ends were adenylated and ligated to the adaptors, followed by ligateion of the 5' adaptors; the library was purified and measured on DNA-concentration
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
The resulted data were demultiplexed using Illumina CASAVA 1.8 and fastq files for each initial sample were generated
Tophat2 alignment of raw paired reads to UCSC mm10 genome
Cuffdiff using the outputs from two previous steps with mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample.
|
| |
|
| Submission date |
Oct 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Poltorak |
| Phone |
6176363596
|
| Organization name |
Tufts University
|
| Street address |
150 Harrison avenue
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02111 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE89361 |
Genome-wide effect of STING-mediated activation in T cells |
|
| Relations |
| BioSample |
SAMN05957535 |
| SRA |
SRX2311561 |
