|
| Status |
Public on Nov 26, 2020 |
| Title |
e49-51hr_faire_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryos
|
| Organism |
Aedes aegypti |
| Characteristics |
strain: Liverpool-IB12 (LVP-IB12)
genotype: wild type
developmental stage: 49-51 hrs after egg laying
tissue: whole embryo
|
| Treatment protocol |
FAIRE was performed using a modified version of the Drosophila melanogaster embryonic tissue protocol (McKay and Lieb, Dev Cell 27:306-318). Samples were crosslinked for 15 min at 60° C, quenched with glycine, and rinsed with buffer A at 4° C. The nuclei were homogenized with a pestle, and the lysate was passed through Miracloth to remove debris.
|
| Growth protocol |
Mosquitoes were maintained in an insectary at 26°C, ~80% humidity, under a 12 hr light and 12 hr dark cycle with 1 hr crepuscular periods at the beginning and end of each light cycle. Mosquito larvae were fed a suspension of dried beef liver powder, while adults were provided cotton soaked with 10% sugar solution. An artificial membrane blood feeding system was utilized to deliver a sheep blood meal to females. Females deposited eggs on paper toweling during two hour eggs collections. Eggs were maintained in the insectary for an additional 49 hrs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were pelleted, resuspended in FAIRE lysis buffer FAIRE Lysis Buffer (2% Triton X-100, 1% SDS, 100mM NaCl, 10mM Tris-Cl pH 8, 1mM EDTA) and subjected to bead beating with 0.5 mm glass beads. Chromatin was sonicated using a Branson 250 ultrasonifier outfitted with a microtip to an average fragment size of 300-500 bp and then phenol-chloroform extracted. 900 ng of FAIRE-enriched DNA was prepared at the University of Notre Dame Genomics and Bioinformatics Core Facility for sequencing on an Illumina HiSeq 2000 sequencer at the BGI Americas Corporation (Cambridge, MA).
FAIRE DNA Illumina libraries were prepared using the TruSeq kit (Illumina) per the manufacturer’s guidelines.
Next-generation Illumina Sequencing (HiSeq 50 bp paired-end sequencing) with a Illumina HiSeq 2000 (BGI Americas Corporation, Cambridge, MA) was used to generate ~150 million reads for each of three replicate FAIRE DNA preparations.
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AaegL3_faire_seq_peaks.narrowPeak
AaegL5_faire_seq_peaks.narrowPeak
|
| Data processing |
FAIRE-Seq reads were cleaned with trimmomatic (CROP:85 HEADCROP:15 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50)
Aligned to the AaegL3.5 and AaegL 5.2 reference genomes using BWA backtrack
Alignments were filtered with SAMtools to remove reads with mapping qualities < 10
Peaks were called with MACS2 (--nomodel -p 0.01 --extsize 550 -g 1.24e9)
Genome_build: AaegL3.5; AaegL5.2
Supplementary_files_format_and_content: peak text files
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL21020 |
| Series (1) |
| GSE162150 |
Updated and validated global cis-regulatory element map which includes the M/m sex-determining region of Aedes aegypti |
|
| Relations |
| BioSample |
SAMN04027489 |
| SRA |
SRX1240815 |
