|
| Status |
Public on May 08, 2024 |
| Title |
RENCA_002_NR_1 |
| Sample type |
SRA |
| |
|
| Source name |
Tumour
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: Tumour
cell type: RENCA
timepoint: day 0
|
| Treatment protocol |
Whole tumours were surgically excised from mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were stored at -80C. RNA was extracted from frozen cells using the RNeasy Plus Micro Kit.
TCRβ amplicon libraries were generated with 5’Rapid Amplification of cDNA Ends (5’RACE) technology. RNA was transcribed to cDNA with a TCRβ constant region primer and a modified SMARTerIIA primer (Integrated DNA Technologies), with 9nt long unique molecular identifiers (UMI) added to individual TCRβ cDNA sequences. TCRβ locus was amplified by nested PCR with an additional TCRβ constant region primers, and a universal primer to SMARTerIIA, with the final PCR adding sequencing adaptors and barcodes to the TCRβ libraries. Products after each PCR were purified using AMPure XP AgenCourt Beads (Beckman Coulter).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Agilent TapeStation for quality control of DNA integrity.
Paired-end (2 × 300 bp) high-throughput sequencing was performed using the Illumina MiSeq platform.
Data processing, aggregation of UMIs and alignment of CDR3 sequences to the IMGT/V-QUEST reference genome were performed using repertoire analysis software based on MIGEC and MiXCR pipelines. Only sequences with UMIs were aligned.
TCRβ clones (defined by the CDR3 amino acid sequence) were excluded if they were less than 8 or greater than 20 amino acids in length, included a stop codon or a frameshift.
Assembly: IMGT/V-QUEST reference genome
Supplementary files format and content: txt files
Supplementary files format and content: clonotype tables
Library strategy: TCR-seq
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
May 08, 2024 |
| Contact name |
Jonathan Chee |
| E-mail(s) |
jonathan.chee@uwa.edu.au
|
| Organization name |
University of Western Australia
|
| Street address |
M503, 35 Stirling Highway
|
| City |
Crawley |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE222575 |
Responders to immune checkpoint therapy display early clonal expansion of tumour-infiltrating lymphocytes |
|
| Relations |
| BioSample |
SAMN32663896 |
| SRA |
SRX18992366 |
