|
| Status |
Public on Dec 22, 2010 |
| Title |
HNF4a_ABdomain_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
HNF4a_ABdomain_ChIPSeq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: hepatocellular carcinoma
chip antibody: HNF4a AB domain
|
| 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 (Part# 0801-0303). 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 HNF4a AB domain
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (Feb, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Nov 12, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenji Daigo |
| E-mail(s) |
daigo@lsbm.org
|
| Phone |
+81-3-5452-5236
|
| Fax |
+81-3-5452-5236
|
| Organization name |
University of Tokyo
|
| Department |
Research Center for Advanced Science and Technology
|
| Lab |
Departments of Molecular Biology and Medicine
|
| Street address |
#35 4-6-1 Komaba
|
| City |
Meguro |
| State/province |
Tokyo |
| ZIP/Postal code |
153-8904 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE18989 |
Genome-wide maps of HNF4a and HNF4g binding state in HepG2 cells. |
| GSE18990 |
Proteomic analysis of native hepatocyte nuclear factor-4{alpha} (HNF4{alpha}) isoforms, phosphorylation status, and interactive cofactors. |
|
| Relations |
| SRA |
SRX018626 |
| BioSample |
SAMN00010744 |
