|
| Status |
Public on Jul 25, 2023 |
| Title |
ChIP_FLAG_flox_adipocytes_day7_LPS |
| Sample type |
SRA |
| |
|
| Source name |
ingSVF-derived adipocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ingSVF-derived adipocytes
genotype: flox
time-course: day 7
treatment: LPS
chip antibody: FLAG M2
|
| Treatment protocol |
At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. When indicated, 20ng/mL LPS was added to the dish 8 hours before sample collection.
|
| Growth protocol |
SVF cells were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were treated by nuclear extraction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 minutes and immediately cross-linked with 1% formaldehyde for 7.5 minutes at room temperature. Cross-linking was quenched using 125 mM glycine for 5 minutes. The chromatin was sheared by probe sonicator (Branson) and was spun at 15,000rpm for 5 minutes. Antibodies were added for overnight incubation at 4C. Mix of Protein A and Protein G magnetic beads (Thermo Scientific) were added to samples for 4h at 4C. Subsequent procedures were performed as described previously (Hiraike Y., Waki H.et.al. 2017).
ChIP-seq libraries were prepared using KAPA hyper prep kit (KAPA Biosystems) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequence reads were mapped to UCSC build mm9 (NCBI Build 37) assembly using bowtie2 (Galaxy version 2.3.4) with default parameters.
Peak calling was performed using MACS2 (Galaxy version 2.1.1.20160309)
Assembly: mm9
Supplementary files format and content: bigWig files showing the peaks of each samples.
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| |
|
| Submission date |
Mar 29, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Yuta Hiraike |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Tokyo
|
| Street address |
Hongo 7-3-1, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1130033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE200194 |
NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis |
| GSE228490 |
NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis [flox ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN33969146 |
| SRA |
SRX19809599 |
