|
| Status |
Public on Jan 01, 2014 |
| Title |
HOT regions are CpG dense promoters in C. elegans and humans |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
ChIP seq of Cfp-1 and H3K4me3 in C. elegans late embryos
|
| |
|
| Overall design |
The coding region of F52B11.1a (cfp-1) was PCR amplified from N2 genomic DNA using Phusion polymerase (Finnzymes) and Gateway cloned into pDONR221. The cfp-1 coding region was then recombined into the MosSCI compatible vector pCFJ201 (which targets Mos site Mos1(cxTi10882) chrIV ) downstream of the dpy-30 promoter and upstream of gfp::tbb-2 3’UTR (Zeiser et al. 2011) to generae strain JA1597 expressing GFP tagged Cfp-1 protein. Late embryos were obtained by aging embryos collected by hypochlorite treatment 3.5 hrs prior to flash freezing in liquid nitrogen. Formaldehyde-fixed chromatin extracts and chromatin immunoprecipitations were as in (Kolasinska-Zwierz et al. 2009) except that DNA was sonicated to a size range of 200-400bp. ChIP assays were performed in 1 ml extract (1 mg protein) in FA buffer with 10 micrograms of anti-GFP rabbit serum (Abcam ab290) and anti-H3K4me3 (Abcam ab8580) individually. DNA sequencing libraries were constructed according using the Illumina Truseq sequencing kit and were sequenced on the Illumina platform.
|
| |
|
| Contributor(s) |
Ahringer J |
| Citation(s) |
24653213 |
| |
| Submission date |
Aug 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Przemyslaw Aleksander Stempor |
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Lab |
Ahringer Lab
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| State/province |
United Kingdom |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
|
| Samples (4)
|
|
| Relations |
| BioProject |
PRJNA215210 |
| SRA |
SRP028813 |
Less...
More...