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Sample GSM809015 Query DataSets for GSM809015
Status Public on Jan 01, 2013
Title H3K27Ac NS ChIP seq
Sample type SRA
 
Source name HUVECs_NS
Organism Homo sapiens
Characteristics cell type: Human umbilical vein cells
passage: within 6 passage
chip antibody: H3K27ac
treatment: none
Treatment protocol 3x10^6 HUVEC cells were plated in 15cm2 culture plate, and cultivated for 3 days. For MEF2C study, cells were stimulated with pitavastatin at a concentration of 1 micro M for 4 hours, and same concentration of DMSO was used as a control sample. For H3K27ac study, cells were harvested without stimulation.
Growth protocol Human umbilical vein endothelial cells (HUVECs) (Lonza, Basel, Switzerland) were cultured in EGM2MV medium (Lonza). HUVECs were used within the first 6 passages.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against H3K27ac
Data processing Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) and alignment files (.bed) were generated using QuEST 2.4 with the following parameters.
For MEF2C
positive_region_size : 300
KDE_bandwidth : 30
ChIP_seeding_fold_enrchment : 30
ChIP_extension_fold_enrichment : 3
ChIP_to_background_fold_enrichment : 3
For H3K27Ac
positive_region_size : 1000
KDE_bandwidth : 100
ChIP_seeding_fold_enrchment : 30
ChIP_extension_fold_enrichment : 3
ChIP_to_background_fold_enrichment : 3
 
Submission date Oct 05, 2011
Last update date May 15, 2019
Contact name Takahide Kohro
E-mail(s) kohro@lsbm.org
Phone 81-3-5452-5237
Organization name LSBM, RCAST
Street address
City 4-6-1, Komaba, Meguroku
State/province Tokyo
ZIP/Postal code 153-8904
Country Japan
 
Platform ID GPL9052
Series (1)
GSE32644 Genome-wide maps of MEF2C and H3K27ac localization in HUVECs
Relations
SRA SRX100255
BioSample SAMN00738197

Supplementary file Size Download File type/resource
GSM809015_HUVEC_H3K27Ac.bed.gz 273.7 Mb (ftp)(http) BED
GSM809015_HUVEC_H3K27Ac.wig.gz 126.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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