 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 04, 2023 |
| Title |
Transcriptomic profiling of ccRCC nephrectomy samples by PCR-cDNAseq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. Following primary tumour resection approximately 30% of patients experience disease recurrence associated with metastasis. To date, long-read RNA sequencing has not been applied to kidney cancer. Here, we used ONT long-read PCR-cDNAseq to profile the transcriptomes of ccRCC archival tumours, 6 of which were from patients who went on to relapse. Our results revealed a loss of immune infiltrate in tumours of patients who relapse. Moreover, thousands of novel isoforms were discovered, including a novel PD-L1 transcript encoding for the soluble version of the protein but having a longer 3'UTR than the currently annotated transcript. Finally, we have identified a novel non-coding gene that was over-expressed in patients who experience recurrence. Our data shows that ONT long-read PCR-cDNAseq can be used in archival tumour samples to comprehensively characterise tumour transcriptomes, and to reveal novel features that would have been missed by short-read RNAseq.
|
| |
|
| Overall design |
RNA was extracted from nephractomy samples, with 2 μg of total RNA per sample used as input for sequencing library preparation (PCS111). Each library was loaded on individual PromethIon flow cell (R9) and sequenced for 72h. Reads with Q >7 were used for subsequent bioinformatic analysis.
|
| |
|
| Contributor(s) |
Lee J, Snell E, Brown J, Banks RE, Vasudev NS, Lagos D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Sep 01, 2023 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Joshua Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
University of York
|
| Department |
Hull York Medical School
|
| Street address |
University Road
|
| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA1011977 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE242204_RAW.tar |
58.2 Mb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...