|
| Status |
Public on Jun 14, 2017 |
| Title |
HDAC3ff_5pm_29C_14 |
| Sample type |
SRA |
| |
|
| Source name |
Brown adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: HDAC3 floxed
time: 5pm
temperature: 29C
|
| Treatment protocol |
Male mice were allowed to acclimate for 2 weeks at thermoneutrality prior to tissue harvest. Mice were acclimated to 29C in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle.
|
| Growth protocol |
Male wild-type and HDAC3 KO mice maintained on a C57BL/6 background maintained on a 12 hour dark /light cycle and were sacrificed at 5PM (ZT10) at 12 weeks of age for the collection of interscapular brown adipose tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated, snap frozen, and thawed directly in Trizol reagent prior to bead homogenization at 4C. RNA was isolated with Qiagen's RNeasy Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation (Part# 2001-2002). The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the UCSC mm9 using Tophat2. For differential gene expression analysis, raw read counts were measured within RefSeq genes using featureCounts, and exact test was performed using edgeR pipeline. Genes were considered for differential expression analysis only if their expression levels are > 0.5RPKM in at least three replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing edgeR differential analysis results and individual replicates expression levels
|
| |
|
| Submission date |
Jun 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hee-Woong Lim |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Division of Biomedical Informatics
|
| Street address |
3333 Burnet Ave. MLC 7024
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE83927 |
Histone Deacetylase 3 Prepares Brown Adipose Tissue For Acute Thermogenic Challenge [RNA-Seq] |
| GSE83928 |
Histone Deacetylase 3 Prepares Brown Adipose Tissue For Acute Thermogenic Challenge |
|
| Relations |
| BioSample |
SAMN05334775 |
| SRA |
SRX1890336 |
