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| Status |
Public on Sep 04, 2023 |
| Title |
329, nephrectomy (PCR-cDNAseq) |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nephractomy samples were first homogenised in QIAzol using stainless steel beads and TissueLyser LT (Qiagen). Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) with an additional Dnase I digestion (QIAGEN) according to manufacturer's instruction.
200ng of total RNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Data processing |
RNAseq reads with a minimum MinKNOW read quality threshold of Q>7 were orientated by pychopper (version 2.5.0), filtered for the presence of 5' and 3' sequencing adpators and trimmed by cutadapt (version 4.1). mapped to hg38 with minimap2 (version 2.24) using the recommended parameters for Oxford Nanopore Technologies long-read sequencing (-ax splice -uf -k14). Samtools (version 1.16) was used to filter out low mapping quality alignments (MAPQ < 10). Reads per gene were counted using featureCounts (version 2.0.0) with long-read counting mode (-L).
Assembly: hg38
Supplementary files format and content: Tab-delimited count matrix files containing sequence read counts mapped to the reference genome
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| Submission date |
Sep 01, 2023 |
| Last update date |
Sep 04, 2023 |
| Contact name |
Joshua Lee |
| E-mail(s) |
josh.lee@york.ac.uk
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| Organization name |
University of York
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| Department |
Hull York Medical School
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| Street address |
University Road
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| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE242204 |
Transcriptomic profiling of ccRCC nephrectomy samples by PCR-cDNAseq |
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| Relations |
| BioSample |
SAMN37234771 |
| SRA |
SRX21600731 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7754994_329.tsv.gz |
4.8 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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