|
Status |
Public on Mar 31, 2013 |
Title |
ETS1 Input |
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 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 |
SRX189746 |
BioSample |
SAMN01731059 |