|
| 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 |
