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| Status |
Public on Nov 16, 2024 |
| Title |
UTUC4 |
| Sample type |
SRA |
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| Source name |
UTUC tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: UTUC tissue
genotype: cancer
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sample stored in RNAlater (-20 °C) using the RNeasy mini kits (QIAGEN).
The 100-bp RNA fraction was utilized to construct cDNA libraries using the TruSeq Stranded mRNA Prep kit (Illumina), following the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
UTUC_4
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| Data processing |
Gene expression values for tumor samples were estimated from the RNA-seq data using the Genomon pipeline (https://github.com/ Genomon-Project/genomon-docs/tree/v2.0).
Alignment was performed using the STAR aligner (v.2.5.2a) against the hg19 human genome.
The BAM files, named Aligned.sortedByCoord.out.bam, which were generated via STAR, were utilized to quantify expression data using GenomonExpression.
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each Sample
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| Submission date |
Aug 26, 2024 |
| Last update date |
Nov 16, 2024 |
| Contact name |
Akinaru Yamamoto |
| E-mail(s) |
[email protected]
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| Phone |
0668793531
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| Organization name |
Osaka University Graduate School of Medicine
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| Street address |
Yamadaoka, 2-2
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| City |
Suita |
| State/province |
Outside U.S./Canada |
| ZIP/Postal code |
N/A |
| Country |
Japan |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE275638 |
RNA sequencing for human upper tract urothelial carcinoma (UTUC) tissue from Japanese patients |
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| Relations |
| BioSample |
SAMN43364679 |
| SRA |
SRX25824856 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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