|
| Status |
Public on Nov 09, 2023 |
| Title |
Normoxia IP #1 |
| Sample type |
SRA |
| |
|
| Source name |
Pulmonary arterial endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Pulmonary arterial endothelial cells
treatment: Normoxia
control: No
|
| Treatment protocol |
Experiments were performed at passages 5 to 8. Cultured HPAECs were either under normoxia or hypoxia (0.2% oxygen) for 24 hours.
|
| Growth protocol |
Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed, crosslinked, and sonicated to get soluble chromatin for immunoprecipitation. 10% input of crosslinked DNA was saved while the remining DNA was precipitated with histone 3 lysine 4 antibody (H3K4Me3, Abcam, ab8580) or non-immune rabbit IgG (Pierce magnetic ChIP kit). Chromatin/antibody complex was then pulled down using Protein A/G Magnetic Beads (Pierece).
DNA samples were proceeded with ChIP-sequencing (sequencing platform: DNBSeqTM, 20M reads).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
2_1
|
| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using STAR v2.7.9a
peaks were called using MACS2 v2.2.7.1
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak peak calls
|
| |
|
| Submission date |
Dec 15, 2021 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Adam Handen |
| E-mail(s) |
adam.handen@gmail.com
|
| Organization name |
University of Pittsburgh
|
| Department |
Vascular Medicine Institute
|
| Lab |
Chan Lab
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL28038 |
| Series (2) |
| GSE191027 |
Genome-wide maps of H3K4Me3 histone modification in human pulmonary endothelial cells under hypoxia |
| GSE232799 |
H3K4me3, mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with KMT2E-AS1 siRNA |
|
| Relations |
| BioSample |
SAMN24108449 |
| SRA |
SRX13423568 |
