GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2319599 Query DataSets for GSM2319599
Status Public on May 03, 2017
Title RNA-RB-X2
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-X2
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
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
BioSample SAMN05785408
SRA SRX2173024

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap