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Sample GSM2254332 Query DataSets for GSM2254332
Status Public on Sep 12, 2016
Title MonkeyRetina-1 11
Sample type SRA
 
Source name WT Monkey Retina 1
Organism Macaca fascicularis
Characteristics strain: WT
tissue: Whole Retina
genotype: Wild Type
Extracted molecule total RNA
Extraction protocol Library preparation for isolated eye and retinal tissue in RNALater, obtained macaque species, was performed similarly to that used for rodent tissues except for the larger scale homogenization required. Macaque samples were each prepared from one eye. Biological replicates were prepared for Macaca fasicularis eye and retina samples.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description Isolated retina mRNA
Monkey_Retina-1
Data processing Prepared libraries of Macaca fasicularis were sequenced by paired-end sequencing with the Illumina Genome Analyzer IIx or HiScan SQ. Data for Macaca fasicularis were processed and aligned with the University of California–Santa Cruz (UCSC; Santa Cruz, CA, USA) rhesus (rheMac3) genome assembly and transcript annotations, respectively, using the Genomic Short-read Nucleotide Alignment Program (GSNAP), manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation of RPKM statistics by gene.
Genome_build: rheMac3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample
 
Submission date Jul 27, 2016
Last update date May 15, 2019
Contact name Xiaodong Bai
Organization name Case Western Reserve University
Department Center for RNA Molecular Biology
Street address 10900 Euclid Avenue
City Cleveland
ZIP/Postal code 44212
Country USA
 
Platform ID GPL17720
Series (1)
GSE84929 RNA-Seq of eye tissues from Monkey eye and retina samples
Relations
BioSample SAMN05449784
SRA SRX1981352

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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