|
| Status |
Public on Nov 09, 2012 |
| Title |
RNASeq_Mouse_Liver_Rep1_ZT10 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
age: Adult (3-6months)
rep: 1
time: ZT10
|
| Treatment protocol |
Mouse were exposed to a 12h light: 12h dark cycle (LD12:12) for at least 2 weeks before the experiment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse liver were removed, cut into small pieces, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used with 4 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA v1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat with the following criteria: -m 1 -F 0 -g 1 --microexon-search --no-closure-search. Reads that map uniquely to the genome were only considered for analysis.
For each gene, reads mapped to exons were summed and normalized to the length of exons. The value, corresponding the read per base pair (rpbp) for any given gene, was normalized to the sequencing depth of each sample (time point).
Normalized rpbp were then used to assess for rhythmic expression. Rhythmically expressed genes with 24hr period were identified by Fourier transformation. The 24hr spectral power (F24) score and its significance (p-value; generated via comparison with a randomly permuted dataset) were obtained using a custom-written R code.
bedGraph files were generated using custom-written perl scripts for visualization purpose only.
Genome_build: mm9
Supplementary_files_format_and_content: RNASeq_Mouse_Liver_NormalizedGeneSignal.txt (a tab-delimited text file) includes Normalized Reads per Base Pair values for each Sample [Linked as supplementary file on Series record.]
Supplementary_files_format_and_content: bedGraph files (generated using custom-written perl scripts) are provided for visualization on Genome Browsers.
|
| |
|
| Submission date |
Mar 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jerome S Menet |
| E-mail(s) |
menet@bio.tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Dept of Biology
|
| Street address |
301 Old Main Drive, Building 1530, ILSB
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE36871 |
Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [RNA-Seq] |
| GSE36916 |
Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation |
|
| Relations |
| SRA |
SRX131972 |
| BioSample |
SAMN00845033 |
