|
| Status |
Public on Sep 30, 2022 |
| Title |
C. elegans L4 hypodermal RNA polymerase DamID |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774
|
| |
|
| Overall design |
Two replicas of control strain BN561 (GFP::Dam in hypodermis) and two replicas of strain BN1414 (Dam::RPB-6 in hypodermis).
|
| |
|
| Contributor(s) |
Askjaer P, Fragoso-Luna A, Romero-Bueno R |
| Citation(s) |
36321973 |
| |
| Submission date |
Sep 27, 2022 |
| Last update date |
Nov 10, 2022 |
| Contact name |
Peter Askjaer |
| E-mail(s) |
[email protected]
|
| Organization name |
Andalusian Centre for Developmental Biology
|
| Street address |
Universidad Pablo de Olavide, Carretera de Utrera, km 1
|
| City |
Seville |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platforms (1) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
|
| Samples (4)
|
|
| Relations |
| BioProject |
PRJNA884838 |
Less...
More...