|
| Status |
Public on Apr 17, 2024 |
| Title |
ATAC-seq in fish 30 hpf cloaca replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
cloaca
|
| Organism |
Danio rerio |
| Characteristics |
tissue: cloaca
Sex: N/A
Stage: 30 hpf
genotype: wild type
strain: AB, Tu, TL
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse and fish tissues were isolated and placed into 1x PBS containing 10% FCS on ice. Collagenase (Sigma-Aldrich C9697) was added to 50ug/ml and incubated at 37ยบ for 20 minutes with shaking at 900rpm.
Cells were washed 3x in 1x PBS. The number of cells was counted and viability confirmed to be greater than 90%. An input of 50000 cells was then processed according to previous description.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ATAC-seq paired-end reads were processed with CutAdapt version 4.1 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 for mouse samples and danRer11 where alternative contigs were removed for fish samples with bowtie2 version 2.4.5 with the following parameters: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000. Only pairs mapping concordantly outside of mitochondria were kept (Samtools v1.16.1)
PCR duplicates were removed by Picard version 3.0.0 (http://broadinstitute.github.io/picard/index.html). BAM files were converted to BED with bedtools version 2.30.0. Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B. Coverages were normalized to million mapped reads.
Assembly: mm39
Assembly: danRer11
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads
|
| |
|
| Submission date |
Dec 15, 2023 |
| Last update date |
Aug 12, 2024 |
| Contact name |
Aurelie Hintermann |
| E-mail(s) |
aur.hin@gmail.com
|
| Organization name |
University of Geneva
|
| Department |
Genetics and Evolution
|
| Street address |
30 quai Ernest-Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL20828 |
| Series (2) |
| GSE250263 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ATAC-seq] |
| GSE250267 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS |
|
| Relations |
| BioSample |
SAMN38851754 |
| SRA |
SRX22897314 |
