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| Status |
Public on Jul 12, 2012 |
| Title |
H3K4me3 normoxia ChIP-seq |
| Sample type |
SRA |
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| Source name |
H3K4me3 normoxia ChIP-seq
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HUVEC
chip antibody: H3K4me3 [kindly provided by Dr Kimura CMA304 (Cell Struct Funct. 2008;33(1):61-73)]
passage: within 6 times
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| Growth protocol |
HUVECs are cultured under normoxia(20% oxygen) and hypoxic (1% oxygen) condition for 24hrs.
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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 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 16 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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| Data processing |
All unique mapped sequences were analyzed by QuEST 2.4 software.
QuEST software was conducted according to the QuEST recommendations and added with FDR analysis in QuEST procedure.
The following paramters were used : positive region size=1000, KDE bandwidth=100, ChIP seeding fold enrichment=10, ChIP extension fold enrichment=3, ChIP-to-background fold enrichment=3.
Genome_build: hg18
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| Submission date |
Jul 03, 2012 |
| 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) |
| GSE39089 |
Genome-wide binding sites of Hypoxia inducible factor 1 (HIF1) and histone modifications |
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| Relations |
| SRA |
SRX157613 |
| BioSample |
SAMN01085429 |
| Named Annotation |
GSM955983_HUVEC_H3K4me3_Normoxia.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM955983_HUVEC_H3K4me3_Normoxia.wig.gz |
99.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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