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| Status |
Public on Nov 02, 2019 |
| Title |
Non-SCCB4 |
| Sample type |
SRA |
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| Source name |
Clinical Non-SCCB sample
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Non-SCCB (urothelial carcinoma)
sample type: Archived FFPE samples
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| Growth protocol |
For bladder-PARCB cell lines, cells were cultured in stem cell culture medium in regular tissue culture flask. The cells grow in suspension condition.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For clinical samples, using Ambion RecoverAll kit (Thermofisher, #AM1975); For Bladder-PARCB cells, using Qiagen miRNeasy kit (Qiagen, #217004)
Human FFPE RNA-seq kit (Nugen, #0341-32)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Raw reads were mapped to hg38 human genome using TOIL
Transcripts were quantified by expectation-maximization (RSEM), TPM was calculated
Gene list was filtered for HUGO coding genes
Supplementary_files_format_and_content: TPM-HUGO-FFPE.txt: the TPM matrix for clinical samples; TPM-HUGO-Bladder-PARCB.txt: the TPM matrix for Bladder-PARCB cell lines
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| Submission date |
Nov 01, 2019 |
| Last update date |
Nov 06, 2019 |
| Contact name |
Liang Wang |
| E-mail(s) |
liangwang@mednet.ucla.edu
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| Organization name |
UCLA
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| Department |
MIMG
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| Lab |
Owen Witte
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| Street address |
675 Charles E Young Dr
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE139822 |
RNA-seq data of small cell carcinoma of the bladder (SCCB) /urothelial carcinoma (Non-SCCB) clinical samples, and bladder-PARCB cell lines |
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| Relations |
| BioSample |
SAMN13176409 |
| SRA |
SRX7085314 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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