|
| Status |
Public on Aug 31, 2012 |
| Title |
Sample 6_whole transcriptome (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
whole transcriptome (RNA-seq)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
gender: male
genotype/variation: wild-type
tissue: liver
time: CT20
molecule subtype: rRNA depleted total RNA
|
| Growth protocol |
Male C57BL/6J at 8-12 weeks of age were housed in light-tight boxes and entrained to LD12:12 conditions. After a minimum of 7 days, animals were transferred to constant darkness (DD) conditions. Thirty-six hours after DD, liver samples (N=3 mice) were collected every 4 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from livers using Trizol reagent according to the manufacturer’s instructions (Life Technologies).
10 μg of total RNA pooled from three mice (individual mouse RNA samples with RIN values of 8-9) was depleted of ribosomal RNAs using RiboMinus Eukaryote Kit for RNA-seq according to the manufacturer’s instructions (Life Technologies).
The removal of ribosomal RNAs was confirmed on a Bioanalyser Pico Chip (Agilent). Sequencing libraries were constructed using SOLiD Total RNA-seq Kit (Life Technologies) with a modification below.
A total of 1 μg of rRNA-depleted total RNA was fragmented in the 30 μl of T4 PNK buffer for 18 min at 95°C and placed on ice immediately.
Fragmented RNA was phosphorylated by adding 2 μl of T4 PNK and 1 mM ATP for 60 min at 37°C and purified by RiboMinus Concentration module (Life Technologies) prior to the adaptor ligation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
Sequence reads were mapped to the mouse genome (NCBI m37/mm9) with Applied Biosystems BioScope v1.3 to create Wig and BigWig files for visualization on the UCSC Genome Browser.
Wig files were normalized to display uniquely mapped reads per 10 million total number of reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Aug 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph S Takahashi |
| E-mail(s) |
[email protected]
|
| Phone |
214-648-1876
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
HHMI, Neuroscience
|
| Lab |
Joseph S. Takahashi
|
| Street address |
5323 Harry Hines Blvd., NA4.118
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
| |
|
| Platform ID |
GPL14602 |
| Series (2) |
| GSE39860 |
Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals |
| GSE39978 |
Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [RNA-seq] |
|
| Relations |
| SRA |
SRX174609 |
| BioSample |
SAMN01109312 |
