|
| Status |
Public on Jul 02, 2024 |
| Title |
Control_22C_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
interscapular BAT
|
| Organism |
Mus musculus |
| Characteristics |
tissue: interscapular BAT
genotype: HDAC3 floxed on C57BL/6J, male
treatment: Room Temperature 22C
|
| Treatment protocol |
Male mice housed at 22C were subjected to cold exposure to 15C for 24 hours in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle. After that, they were housed at 22C for 1 or 7 days. Room temperature (22C) cohorts were maintained in standard housing room.
|
| Growth protocol |
Male HDAC3 floxed and Ucp1-cre HDAC3 floxed mice on a C57BL/6 background maintained on a 12 hour dark /light cycle and were sacrificed at 5PM (ZT10) at 10-12 weeks of age for the collection of interscapular brown adipose tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from snap-frozen BAT using TRIzol reagent (Thermo Fisher Scientific, 15596026) followed by RNeasy Mini Kit (QIAGEN, 74104).
Total RNA was isolated from mouse interscapular BAT of 10-12-week old mice. 250 ng of total RNA from biological replicates were DNase-treated prior to rRNA removal completed with a Ribo-Zero Magnetic kit (Illumina, MRZH11124) per standard protocol. The RNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, RS-122-2001) according to the standard Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HDAC3_Control_22C_65040
|
| Data processing |
RNA-seq reads were aligned to UCSC mouse genome, mm9, using STAR aligner. Only uniquely aligned reads were retained for downstream analysis. Read count for each gene and samples were counted using FeatureCounts. Differential analysis was performed using EdgeR.
Assembly: mm9
Supplementary files format and content: EdgeR_results
|
| |
|
| Submission date |
Sep 29, 2023 |
| Last update date |
Jul 02, 2024 |
| Contact name |
Mohit K. Midha |
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE244385 |
Short-term cold exposure induces persistent epigenomic memory in brown fat [RNA-Seq] |
| GSE244386 |
Short-term cold exposure induces persistent epigenomic memory in brown fat |
|
| Relations |
| BioSample |
SAMN37610673 |
| SRA |
SRX21946849 |
