|
| Status |
Public on May 05, 2024 |
| Title |
ND_hypoxia_input_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Bone marrow derived macrophages
cell type: Macrophages
genotype: WT
treatment: Normal diet_hypoxia
chip-ab: IgG (171870)
|
| Treatment protocol |
Cells were cultured in 1% O2 hypoxia chamber for 1 hour at day7.
|
| Growth protocol |
BMDMs were derived from whole bone marrow cells and were cultured in DMEM with 10% FBS, pen/strep and 20ng/ml of M-CSF at 37C at 5% CO2. Media was changed to Macrophage-SFM with 20ng/ml of M-CSF at day4.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 0.4% paraformaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs. 2 ng of DNA was used as starting material for input and ip samples. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The fastq files were processed using PartekFlow (Partek Inc., St. Louis, MO, USA).
The raw reads were aligned to mm10 with Bowtie2 and peaks were called by MACS2 with the significance cut-off q-value <=0.05.
Called peaks were quantified to regions and the normalization was performed with transcripts per million (TPM). The normalized peaks were then subjected to statistical analysis using Partek gene-specific analysis (GSA). Differential H3K4me3 peaks were identified with thresholds (p<0.05, least square mean > 20).
narrowpeak files were generated using MACS2 with default setting. Bigwig files were generated using bamCoverage on Galaxy.
Assembly: mm10
Supplementary files format and content: narrowpeak (except for Input sample)
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Norifumi Urao |
| Organization name |
SUNY Upstate Medical University
|
| Department |
Pharmacology
|
| Street address |
750 E. Adams St.
|
| City |
Syracuse |
| State/province |
New York |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE231991 |
Diet-induced obesity dysregulates rapid epigenetic response to hypoxia in macrophages (ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN35002815 |
| SRA |
SRX20258037 |
