|
| Status |
Public on Oct 15, 2021 |
| Title |
hSMC_5hmc_INPUT |
| Sample type |
SRA |
| |
|
| Source name |
Aortic SMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Aortic SMC
hmedip antibody: none
fraction: INPUT sample
|
| Treatment protocol |
hCASMC were treated with 50nM rapamycin for 48 hours
|
| Growth protocol |
Human coronary artery smooth muscle cells (hCASMCs, Lonza) were propagated in M199 medium (Gibco, 11150-067) supplemented with 10% FBS, 100 U/ml each penicillin-streptomycin, 2.7 ng/ml rhEGF (Biolegend, 713008), and 2ng/ml rhFGF (Biolegend, 71034). Before treatment, SMC were starved at 2.5% serum for 24 hours.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
hydroxymethylated DNA was immunoprecipitated by Hydroxymethylated DNA IP Kit (Diagenode) following manufacturer's protocol. Precipitated genomic DNA was sonicated to 200 – 500 bp using the Covaris sonicator. 1 µg of fragmented genomic DNA was immunoprecipitated with a 5-hmC monoclonal antibody using the hMeDIP kit (Diagenode). The DNA-antibody mixture was then incubated with magnetic beads overnight at 4°C, washed and DNA purified using purification kit (Qiagen, 69504)
DNA library was prepared by NEBNext DNA library prep Master Mix set for illumina 6040 and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) E7335.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Rap48_chipseeker.xlsx
|
| Data processing |
Library strategy: hMeDIP-seq
Raw reads were aligned to hg38 using Bowtie2 after quality control. Peaks were called using MACS2 callpeak with cut off FDR (q-value) < 0.05 and INPUT files were used as the control group. Peaks were annotated by ChIPseeker with hg38.ncbiRefSeq as the annotation source.
Genome_build: Hg38
Supplementary_files_format_and_content: Annotated peak file
|
| |
|
| Submission date |
Jun 30, 2021 |
| Last update date |
Oct 15, 2021 |
| Contact name |
Delphine Gomez |
| E-mail(s) |
gomezd@pitt.edu
|
| Phone |
412-383-3269
|
| Organization name |
University of Pittsburgh
|
| Department |
Medicine, division of Cardiology
|
| Lab |
Delphine Gomez Lab
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE179219 |
H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [hMeDIP-seq] |
| GSE179220 |
H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis |
|
| Relations |
| BioSample |
SAMN19976669 |
| SRA |
SRX11318254 |
