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| Status |
Public on Feb 02, 2016 |
| Title |
Effect of Bmal1 post-natal knockout on liver gene expression: time-series |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Gene expression in the liver has been studied extensively in normal mice, but not in mice with circadian disruption. We use a tamoxifen-inducible Lox/Cre KO mouse strain with the most important clock gene knocked out, BMAL-1. The aim of this experiment was to study the effect of circadian disruption on gene expression in the liver by comparing conditional Bmal1 KO mice with WT mice using RNA-seq. All mice were housed under 12h:12h LD conditions with free access to food and water. Seven days after the last dose of tamoxifen, mice were kept under constant darkness for 36 h and then sacrificed. Four mice per genotype were sacrificed in darkness every 4h for 20h (6 time points). Illumina TruSeq RNA Sample Prep v2 was used for library construction and samples were sequenced on an Illumina HiSeq 2000. RNA-seq data were aligned by STAR, and data were normalized with a resampling strategy (https://github.com/itmat/Normalization).
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| Overall design |
Time-series liver mRNA profiles of 4- to 6-month-old male wild type (WT) and Bmal1 knockout (KO) mice were generated by sequencing, four mice per genotype per timepoint, using Illumina HiSeq 2000.
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| Contributor(s) |
Yang G, Paschos GK, Grant GR, Grosser T, FitzGerald GA, Chen L |
| Citation(s) |
26843191 |
| |
| Submission date |
Jul 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregory Robert Grant |
| E-mail(s) |
ggrant@upenn.edu
|
| Phone |
215-573-3736
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| Organization name |
University of Pennsylvania
|
| Department |
Genetics
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| Lab |
ITMAT Bioinformatics
|
| Street address |
3400 Civic Center Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (48)
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| Relations |
| BioProject |
PRJNA288820 |
| SRA |
SRP060295 |
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