|
| Status |
Public on Feb 05, 2014 |
| Title |
Rat retina, Time series, ZT7 (mid-day) |
| Sample type |
SRA |
| |
|
| Source name |
Rat retina, ZT7 (mid-day)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: Retina
animals in pool: 10
time of day: ZT7 (mid-day)
age: 6-8 weeks
|
| Treatment protocol |
Rats were housed in 14:10 lighting cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol, followed by clean-up using RNeasy Micro kit with on-column DNase treatment. Quantitation and quality assuance were performed using a NanoDrop and Bioanalyzer, respectively.
A SPRI-TE kit (Beckman-Coulter) was used wherein 10 µg of total RNA was polyA-RNA-enriched using streptavidin-coated magnetic beads, followed by Covaris RNA fragmentation. Fragmented RNA was used to generate cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was ligated to Illumina paired end (PE) adaptors containing a 6-basepair bar-code. Size selection was performed using a Pippin Prep 1.5% cartridge. Libraries were enriched using 16 cycles of PCR and purified using Ampure XP Beads (Agencourt). Each library was run as one of six bar-coded samples per lane on an Illumina HiSeq machine yielding paired-end, 101-base sequencing reads. Image analysis and base calling were done using RTA1.12.4.2 and CASAVA1.8.0.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Image analysis and base calling were done using RTA1.12.4.2 and CASAVA1.8.0.
RNA-Seq reads were aligned to the rn4 genome assembly using Tophat-1.3.1.Linux_x86_64
FPKM values were calculated using Cufflinks-1.2.0.Linux_x86_64
Genome_build: rn4
Supplementary_files_format_and_content: FPKM abundance measurements
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven Coon |
| E-mail(s) |
coons@mail.nih.gov
|
| Phone |
3014516622
|
| Organization name |
NIH
|
| Department |
NICHD/PDEGEN
|
| Lab |
Section on Neuroendocrinology
|
| Street address |
49 Convent Drive Room 6A83
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-4510 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE46069 |
Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle |
|
| Relations |
| SRA |
SRX265402 |
| BioSample |
SAMN02045894 |
