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| Status |
Public on Dec 01, 2017 |
| Title |
PC-3_WCE_01 |
| Sample type |
SRA |
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| Source name |
Xenograft
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human prostate cancer cell line
cell line: PC-3
treatment duration: 10 weeks
host strain: nude mice
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were removed, flash frozen on dry ice, and RNA was harvested using Zymo research RNA kit.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA kits.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
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| Description |
Sample 4
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| Data processing |
RNA-seq reads were aligned to mm10 genome assembly using Tophat version 2.0.13 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jun 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chin-Hsien Tsai |
| E-mail(s) |
tch@gate.sinica.edu.tw
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| Organization name |
Academia Sinica
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| Department |
ABRC
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| Street address |
Nan-Kang
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| City |
Taipei |
| State/province |
Others |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
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| Platform ID |
GPL15456 |
| Series (1) |
| GSE99820 |
Effects of WCE herbal extract on hormone-refractory PC-3 tumors |
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| Relations |
| BioSample |
SAMN07190893 |
| SRA |
SRX2881690 |
| 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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