|
| Status |
Public on Aug 20, 2024 |
| Title |
1832_D28_Ctrl_pos |
| Sample type |
SRA |
| |
|
| Source name |
T lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
lmp2 specificity: positive
days in culture: 28
treatment: Untreated
|
| Treatment protocol |
Cells were treated or not with anti-PD-L1 and anti-TIM3 antibodies.
|
| Growth protocol |
Cells were stimulated weekly with LMP2-pulsed dendritic cells and cultured in complete media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS-sorted LMP2 multimer-positive and multimer-negative T cells were harvested. RNA was isolated using Trizol reagent in combination with the PureLink RNA mini and microcolumn system.
Oncomine™ TCR Beta-SR Assay for RNA was used for the construction of sequencing libraries. Sequencing was completed on the Ion S5 semiconductor platform using an Ion 540 chip.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Data processing |
Ion Reporter software (version 5.12) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 whole genome using the Ion Reporter software (version 5.12).
Counting data of referenced clones were generated by the Ion Reporter software (version 5.12).
Genome_build: hg19
Supplementary_files_format_and_content: Coma-separated value files include VDJ genes associated with CDR3 amino acid and nuclotide sequences, read counts, and read proportions for each sample.
|
| |
|
| Submission date |
Aug 21, 2021 |
| Last update date |
Aug 20, 2024 |
| Contact name |
Jean-Sebastien Delisle |
| E-mail(s) |
js.delisle@umontreal.ca
|
| Phone |
514-252-3400
|
| Organization name |
Centre de recherche de l'Hôpital Maisonneuve-Rosemont
|
| Street address |
5415 Boulevard de l'Assomption
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H1T 2M4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE182537 |
TCR beta sequencing in LMP2-positive and LMP2-negative human T cells treated with anti-PD-L1 and anti-TIM3 antibodies. |
|
| Relations |
| BioSample |
SAMN20924021 |
| SRA |
SRX11857416 |
