|
| Status |
Public on Jun 01, 2024 |
| Title |
IP_Effector_IgG |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cell
clip antibody: anti-IgG rabbit antibody (Thermo Fisher Scientific, Waltham, MA, cat. #02-6102)
|
| Treatment protocol |
Cells were UV crosslinked on ice at 400 mJ/cm2 using a Stratagene UV Stratalinker 2400 and sent to Eclipse BioinnovationsInc. for processing using their RBP-eCLIP protocol (RBP-eCLIP Protocol v2.01 R). Immunoprecipitation was performed using the anti-Tra2beta rabbit polyclonal antibody (Santa Cruz Biotechnology, Dallas TX, cat. #sc-166829) and anti-IgG rabbit antibody (Thermo Fisher Scientific, Waltham, MA, cat. #02-6102).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RBP-eCLIP protocol (Eclipsebio RBP-eCLIP Protocol v2.01R)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Total RNA from CD8+ T cells
|
| Data processing |
Sequences were analyzed using the original eCLIP analysis pipeline (Eclipse Data Analysis Protocol). Significant eCLIP peaks (Tra2β binding events) were identified by Clipper using the strict threshold set by Eclipse Bioinnovations of log2 fold change ≥ 3 and -log10(p-value) ≥ 3.
Assembly: mm10
Supplementary files format and content: Bigwig files
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
Jun 04, 2024 |
| Contact name |
Anthony Vella |
| E-mail(s) |
vella@uchc.edu
|
| Organization name |
UConn Health
|
| Department |
Immunology
|
| Lab |
Vella
|
| Street address |
263 Farmington Ave
|
| City |
Farmington |
| State/province |
Connecticut |
| ZIP/Postal code |
06030 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE267587 |
Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [CLIP-seq] |
| GSE267609 |
Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate |
|
| Relations |
| BioSample |
SAMN41408694 |
| SRA |
SRX24569003 |
