|
| Status |
Public on Nov 26, 2020 |
| Title |
Updated and validated global cis-regulatory element map which includes the M/m sex-determining region of Aedes aegypti |
| Organism |
Aedes aegypti |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Formaldehyde assisted isolation of regulatory element (FAIRE) enrichment was used to recover open chromatin from A. aegypti embryos. Next-generation sequencing of FAIRE DNA was performed. Computational detection and analysis of FAIRE-enriched DNA sequences followed.
|
| |
|
| Overall design |
For each of three biological replicates, A. aegypti eggs were collected for two hours and aged until 49-51 hrs after egg laying, at which point they were used as starting material for preparation of FAIRE-enriched DNA. The FAIRE DNA enrichment protocol involved formaldehyde crosslinking and shearing of chromatin, followed by phenol chloroform extraction to recover open promoter regions from the aqueous phase. Next-generation Illumina sequencing followed by computational detection and analysis of FAIRE-enriched sequences followed.
|
| |
|
| Contributor(s) |
Nowling RJ, Duman-Scheel M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R21 AI117145 |
Cis-regulatory element discovery in a sequenced mosquito genome |
INDIANA UNIVERSITY |
Molly Duman Scheel |
|
| BioProject |
PRJNA294762 |
| Submission date |
Nov 25, 2020 |
| Last update date |
Nov 26, 2020 |
| Contact name |
Ronald J Nowling |
| E-mail(s) |
nowling@msoe.edu
|
| Organization name |
Milwaukee School of Engineering
|
| Street address |
1025 N Broadway
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53202 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL21020 |
Illumina HiSeq 2000 (Aedes aegypti) |
|
| Samples (3) |
|
| Relations |
| SRA |
SRP063665 |
