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Status |
Public on Jan 01, 2013 |
Title |
H3K27Ac NS ChIP seq |
Sample type |
SRA |
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Source name |
HUVECs_NS
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Organism |
Homo sapiens |
Characteristics |
cell type: Human umbilical vein cells passage: within 6 passage chip antibody: H3K27ac treatment: none
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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.
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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.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
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Description |
Chromatin IP against H3K27ac
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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
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Submission date |
Oct 05, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Takahide Kohro |
E-mail(s) |
kohro@lsbm.org
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Phone |
81-3-5452-5237
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Organization name |
LSBM, RCAST
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Street address |
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City |
4-6-1, Komaba, Meguroku |
State/province |
Tokyo |
ZIP/Postal code |
153-8904 |
Country |
Japan |
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Platform ID |
GPL9052 |
Series (1) |
GSE32644 |
Genome-wide maps of MEF2C and H3K27ac localization in HUVECs |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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