|
| Status |
Public on Jun 03, 2010 |
| Title |
[E-TABM-722] do600_HNF4a_liver_ARP31046_tc1S2_CRI02 |
| Sample type |
SRA |
| |
|
| Source name |
tc1S2
|
| Organism |
Mus musculus |
| Characteristics |
genotype: contains human chromosome 21
strain: TC1
developmentalstage: adult
organismpart: liver
sex: male
individual: tc1S2
chip antibody: HNF4a
chip catalog number: ARP31046
|
| Growth protocol |
TC1 mouse | growth | The protocol describing the mouse strain TC1 can be found at http://0-dx-doi-org.brum.beds.ac.uk/10.1126/science.1114535
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde. After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
chip_seq | sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles. doi:10.1016/j.ymeth.2009.03.001
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
do600_HNF4a_liver_ARP31046_tc1S2_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: HNF4a
Factor Value [GENOTYPE]: contains human chromosome 21
|
| Data processing |
none
|
| |
|
| Submission date |
Jun 01, 2010 |
| Last update date |
Jun 02, 2010 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE22078 |
[E-TABM-722] Transcription factor binding evolution in five vertebrates |
|
