|
| Status |
Public on Aug 01, 2023 |
| Title |
patient5_T0_TCRbeta |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
cell type: tumor-infiltrating lymphocytes (TILs)
patient: patient5
time: pre-ACT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction and as described in Genolet et al., Cell Report Methods, 2013.
Libraries were prepare using targeted TCR amplification
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiniSeq |
| |
|
| Description |
patient5_T0_TCRbeta
|
| Data processing |
Deep sequencing of the TCR beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Assembly: IMGT data base was used to identifiy TCR
Supplementary files format and content: txt files containing the list of TCR and their frequencies
Library strategy: TCR-seq
|
| |
|
| Submission date |
Jun 07, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
David Barras |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre hospitalier universitaire vaudois
|
| Department |
Oncology
|
| Street address |
AGORA, Bugnon 25A
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL22790 |
| Series (2) |
| GSE229861 |
Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma |
| GSE234352 |
Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma [TCR-Seq] |
|
| Relations |
| BioSample |
SAMN35663846 |
| SRA |
SRX20629922 |
