|
| Status |
Public on Apr 15, 2010 |
| Title |
CFP1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Whole Brain
strain: C57BL/6
age: 7 weeks
chip antibody: CFP1 (Sc-25391 – Santa Cruz)
|
| Treatment protocol |
Brains were manually homogenised to a single cells suspension and crosslinked using 1% formaldehyde. Chromatin was sheared using a combination of Micrococcal nuclease and sonication.
|
| Growth protocol |
Whole brains were disected from C57black/6 mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein-DNA complexes were immunoprecipitated with specific antibodies and the DNA was subsequently extracted. Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. 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 CFP1
|
| Data processing |
Alignment: Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained.
|
| |
|
| Submission date |
Oct 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Adrian P Bird |
| E-mail(s) |
A.Bird@ed.ac.uk
|
| Phone |
0131 6508695
|
| Fax |
0131 6505379
|
| Organization name |
The University of Edinburgh
|
| Department |
WTCCB
|
| Lab |
Bird Lab
|
| Street address |
Mayfield Road
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE18578 |
Genome-wide maps of CFP1, RNA Polymerase II and H3K4me3 in mouse brain. |
|
| Relations |
| SRA |
SRX017083 |
| BioSample |
SAMN00009377 |
