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Sample GSM1124039 Query DataSets for GSM1124039
Status Public on Oct 24, 2014
Title Rat pineal gland, post-natal day 5 (P5), mid-night (ZT19)
Sample type SRA
 
Source name Pineal gland
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: Pineal gland
animals in pool: 19
time of day: mid-night (ZT19)
age: post-natal day 5 (P5)
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 assurance were performed using a NanoDrop and Bioanalyzer, respectively.
An NEB Master Mix kit 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 the Ampure XP Beads (Agencourt). Each library was run as one of four 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 RTA1.10.36 and CASAVA1.7.0.
 
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 RTA1.10.36 and CASAVA1.7.0.
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
 
Submission date Apr 16, 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)
GSE46127 Whole transcriptome profiling of the rat pineal gland during development from embryonic day 21 to adult
Relations
BioSample SAMN02046797
SRA SRX266519

Supplementary file Size Download File type/resource
GSM1124039_FPKM_dev_P5N.txt.gz 816.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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