|
| Status |
Public on Jul 20, 2021 |
| Title |
E12.5 wild-type distal forelimb ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
distal forelimb
|
| Organism |
Mus musculus |
| Characteristics |
age: E12.5
strain: B6CBAF1
genotype: wild-type
tissue: distal forelimb
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37ยบ for approximately 5min. Cells were counted and 50,000 cells were isolated for processing with the Nextera Tn5 enzyme (Illumina FC-131-1096) as previously described (Buenrostro NatMeth 2013).
Tn5 treated DNA was amplified with Nextera Library primers using NEBNext library amplification master mix (NEB M0541).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ATAC-seq reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 2000 --fr --dovetail --very-sensitive-local).
Reads with mapping quality below 30, mapping to mitochondria, or not properly paired were removed from the analysis. PCR duplicates were filtered using Picard (v1.56.0).
BAM file was converted to BED with bedtools version 2.27. Peak calling was done using MACS2 (v2.1.0.20151222) callpeak (--nomodel --shift 100 --extsize 200 --call-summits --keep-dup all).
The coverage was done using the center of the Tn5 insertion and extended on both sides by 20 bp (script available at https://github.com/lldelisle/scriptsForBoltEtAl2021)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage centered on the Tn5 insertion (20bp extended both sides)
narrowPeak: narrowPeak from macs2
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jan 20, 2022 |
| Contact name |
Lucille Lopez-Delisle |
| E-mail(s) |
lucille.delisle@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE165490 |
Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [ATAC-Seq] |
| GSE165495 |
Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations |
|
| Relations |
| Reanalyzed by |
GSM5828319 |
| BioSample |
SAMN17531911 |
| SRA |
SRX9934227 |
