|
| Status |
Public on Mar 31, 2013 |
| Title |
H3K27ac Hour 4 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Human Umbilical Vein Endothelial Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Human Umbilical Vein Endothelial Cells
passages: P3-6
treatment: VEGF
time: 4h
chip antibody: H3K27ac
chip antibody manufactuer: Abcam
chip antibody catalog #: Ab4729
|
| Treatment protocol |
HUVEC cells cultured in full EGM2 medium were changed to EBM2 medium (Lonza) with 0.5% FBS overnight. VEGFa (50ug/ml, R&D Systems) was added the next day and samples were collected at 0, 1, 4, and 12 hours
|
| Growth protocol |
Primary HUVEC purchased from Lonza within 3-6 passages were grown in EGM2 medium (Lonza) up to 80%-90% confluence
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq
|
| Data processing |
All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option
All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database
FPKM for all RNA-seq experiments were performed using cufflinks and cuffdiff using the -T option (for time series) and using Ensembl GRCh37 version 65 as a reference transcript annotation (no novel assembly)
Genome_build: hg19
Supplementary_files_format_and_content: The processed FPKM file is CSV file with each row a different Ensembl gene that has the FPKM at each of the 4 time points
Supplementary_files_format_and_content: The BED files for the ChIP-seq and Dnase I samples are all the aligned, non-filtered reads
|
| |
|
| Submission date |
Sep 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE41166 |
A dynamic H3K27ac signature defines VEGF-regulated endothelial enhancers |
|
| Relations |
| SRA |
SRX189718 |
| BioSample |
SAMN01731031 |
