|
| Status |
Public on Oct 19, 2022 |
| Title |
Day 6 differentiating adipocytes H3K27ac ChIP seq WT1 |
| Sample type |
SRA |
| |
|
| Source name |
Inguinal white adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Wild type
|
| Treatment protocol |
Proliferating preadipocytes were replated and grown until confluency. Two days after reaching confulency, Preadipocytes were treated to differentiate into adipocytes using differentiation media (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 4 days and maintained in maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days.
|
| Growth protocol |
Preadipocytes were isolated from inguinal white adipose tissue of WT and DKO mice and cultured on collagen coated plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells for fixed in tissue culture plates with methonol free 1% paraformaldehyde and then collected.
ChIP libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalling was performed using RTA version 2.4.6
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Reads were mapped to UCSC mm10 reference genome using BWA 07.17
Peak detection of enriched binding regions was performed using MACS2 v. 2.1.1.20160309 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Predicted peak files in narrowPeak format
|
| |
|
| Submission date |
Jan 09, 2022 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Michael Bustin |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH
|
| Department |
NCI
|
| Lab |
Laboratory of Metabolism
|
| Street address |
Building 37, Room 3122
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE193333 |
HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity [ChIP-Seq] |
| GSE193463 |
HMGNs Regulate White Adipocyte Browning By Stabilizing Cell Identity |
|
| Relations |
| BioSample |
SAMN24777298 |
| SRA |
SRX13688199 |
