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Sample GSM1122817 Query DataSets for GSM1122817
Status Public on Feb 05, 2014
Title Rat pineal gland, Time series, ZT19 (mid-night)
Sample type SRA
Source name Rat pineal gland, ZT19 (mid-night)
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: Pineal gland
animals in pool: 10
time of day: ZT19 (mid-night)
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
Phone 3014516622
Organization name NIH
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
SRA SRX265399
BioSample SAMN02045891

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

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