|
| Status |
Public on Apr 24, 2022 |
| Title |
Arid1a KO - rep 3, technical rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cells
genotype: Arid1a KO
|
| Treatment protocol |
For c-Myc KO samples, Naïve CD8 T cells were treated with 4OHT for 24hr before activation.
|
| Growth protocol |
Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division CD 8 T cells were sorted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Low input
RNA were isolated by using Direct-zol RNA Microprep Kits (R2061, Zymo Research)
Libraries were prepared using KAP RNA HyperPrep Kit with RiboErase (HMR) (08098131702, Roche) and purified by AMPure SPRI beads (B23318, Beckman-Coulter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
First-division CD8 T cells
|
| Data processing |
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample
Supplementary_files_format_and_content: Raw read counts of feature-sample in csv file
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Douglas R Green |
| E-mail(s) |
douglas.green@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Immunology
|
| Lab |
Green lab
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
United States |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE183615 |
BAF complex cooperates with c-Myc to orchestrate early fate decisions of CD8 T cells (RNA-seq) |
| GSE183619 |
BAF complex cooperates with c-Myc to orchestrate early fate decisions of CD8 T cells |
|
| Relations |
| BioSample |
SAMN21344460 |
| SRA |
SRX12036020 |
