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| Status |
Public on Sep 04, 2023 |
| Title |
382, nephrectomy |
| 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.
2 μg 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 mapped to hg38 with minimap2 (version 2.24) using the recommended parameters for Oxford Nanopore Technologies direct RNA 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 |
Aug 30, 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) |
| GSE241932 |
Transcriptomic profiling of ccRCC nephrectomy samples by Direct RNAseq |
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| Relations |
| BioSample |
SAMN37198706 |
| SRA |
SRX21518920 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7745767_382.tsv.gz |
4.9 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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