|
| Status |
Public on May 03, 2017 |
| Title |
RNA-RB-X4 |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: retinoblastoma xenograft
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RB-X4
|
| Data processing |
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the human genome hg19(GRCh37) using in-house software StrongArm developed from PCGP project.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation v23.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Sep 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
|
| Organization name |
St Jude Children's Research Hosipital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE87042 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [RNA-Seq_Hs] |
| GSE87064 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis |
|
| Relations |
| BioSample |
SAMN05785417 |
| SRA |
SRX2173026 |
