|
| Status |
Public on Jun 09, 2017 |
| Title |
MC20 |
| Sample type |
SRA |
| |
|
| Source name |
liver tumor
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 27
patient age at resection: 30.7
patient sex: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from fresh frozen tissue using the Roche High Pure FFPE kit (Roche Diagnostics). After Ribogreen quantification and quality control via Agilent BioAnalyzer, 0.5 to 1 ug of total RNA underwent stranded TruSeq library preparation according to the manufacturer's instructions (Illumina), with 6 cycles of PCR.
Samples were barcoded and run on a HiSeq 2000 in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina). An average of 69 million paired reads were generated per sample. Ribosomal reads represented at most 0.83% of total reads, while mRNA bases accounted for an average of 61% of reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_02998_MC20
|
| Data processing |
Base calls were made using HiSeq Control Software v.2.0.10.0
Spliced mapping was run with TopHat2 (Bowtie2) to the hg19 genome using the RefSeq gene models from UCSC.
Expression levels were then computed using HTSeq.
Raw expression levels were normalized using Bioconductor package DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: contains HTSeq counts that have been scaled(normalized) using Bioconductor package DESeq
|
| |
|
| Submission date |
Nov 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bic MSKCC |
| Organization name |
Memorial SLoan-Kettering Cancer Center
|
| Street address |
1275 York Ave.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63018 |
Genome and transcriptome profiling of fibrolamellar carcinoma [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN03165785 |
| SRA |
SRX752951 |
