|
| Status |
Public on Jun 20, 2019 |
| Title |
OSKM-NPC_tumor_210 |
| Sample type |
SRA |
| |
|
| Source name |
OSKM-NPC (PSA-NCAM positive)-derived tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: 201B7-derived cells
analysis method: RNA-seq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy plus Mini Kit (QIAGEN) for RNA.
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.16
The sequenced reads were mapped to the hg38 human reference genome using Tophat2 (version 2.1.1) with the human GENCODE (version 27) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
RPKM values were determined by Cufflinks version 2.2.1 package with the human GENCODE (version v27, protein coding) annotation gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include RPKM values for each sample.
|
| |
|
| Submission date |
Aug 16, 2018 |
| Last update date |
Jun 20, 2019 |
| Contact name |
Yasuhiro Yamada |
| E-mail(s) |
yyamada@m.u-tokyo.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Department of Molecular Pathology
|
| Street address |
7-3-1 Hongo, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE118654 |
Human pluripotent stem cell-derived brain tumor model uncovered embryonic stem cell signature as a key driver in atypical teratoid/rhabdoid tumor (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN09843657 |
| SRA |
SRX4560554 |
