|
| Status |
Public on Jul 02, 2024 |
| Title |
HDAC3_KO_7d_Rec |
| Sample type |
SRA |
| |
|
| Source name |
interscapular BAT
|
| Organism |
Mus musculus |
| Characteristics |
tissue: interscapular BAT
genotype: Ucp1-cre HDAC3 floxed on C57BL/6J, male
treatment: Following cold exposure to 15C for 24 hr, mice were housed at 22C for 7 days
|
| 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 |
genomic DNA |
| Extraction protocol |
Interscapular BAT was harvested from individual mice and snap frozen in liquid nitrogen. For each genotype and condition, three biological replicates (individual mouse BAT pads) were thawed on ice and quickly pooled in ice-cold celling buffer A and nuclei isolated on ice by dounce homogenization per GRO-seq nuclei isolation protocol. 5 x 104 isolated nuclei were then washed in ice-cold 1ml of 1x Tagmentation Buffer (2x 20 mM Tris (hydroxymethyl)-aminomethane, 10mM MgCl2, 20% (vol/vol) dimethylformamide, pH 7.6) and resuspended in 50 ml 1x TD buffer prior to the transposition assay. The Nextera DNA Library Prep Kit (Illumina, FC-121-1030) was used for the transposition reaction. The nuclei pellet was resuspended and incubated with transposition reaction mix at 37°C for 30 minutes. DNA was isolated using MinElute Reaction Cleanup kit and eluted in elution buffer (EB).
Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7-9 total cycles. The libraries were purified with AMPure beads (to remove primer-dimers and >1,000 bp DNA fragments) by manufacturer protocol. The library was assessed on an Agilent High Sensitivity DNA Bioanalysis chip and quantitated with the Qubit dsDNA high-sensitivity Assay kit (Thermo Fisher Scientific, Q32851). Libraries were sequenced on an Illumina HiSeq 2000 using 50 bp paired-end (50PE) sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ATAC-seq reads were aligned to UCSC mouse genome, mm9, using STAR aligner with an option “--outFilterMultimapNmax 1 --alignIntronMax 1 --alignMatesGapMax 2000”. Only uniquely aligned reads were retained and deduplicated for downstream analysis. Given that TF-binding open chromatin regions yield short fragments, reads pairs with fragment length < 120bp were selected for downstream analysis. Peak calling and de novo motif search were performed using Homer
Assembly: mm9
Supplementary files format and content: bigWig format
|
| |
|
| 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) |
| GSE244382 |
Short-term cold exposure induces persistent epigenomic memory in brown fat [ATAC-Seq] |
| GSE244386 |
Short-term cold exposure induces persistent epigenomic memory in brown fat |
|
| Relations |
| BioSample |
SAMN37609354 |
| SRA |
SRX21963740 |
