|
| Status |
Public on Jul 20, 2021 |
| Title |
E12.5 inv2 proximal forelimb CR_CTCF |
| Sample type |
SRA |
| |
|
| Source name |
proximal forelimb
|
| Organism |
Mus musculus |
| Characteristics |
age: E12.5
strain: B6CBAF1
genotype: inv2
antibody: anti-CTCF (Active Motif 61311)
tissue: proximal 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 37º for approximately 5min.
DNA isolated from the CUT&RUN protocol were prepared with KAPA HyperPrep reagents (07962347001) with 2.5ul of adaptors at 0.3uM and ligated for 1 hour at 20ºC. The DNA was amplified for fourteen cycles. Post-amplified DNA was cleaned and size selected using 1:1 ration of DNA:Ampure SPRI beads (A63881) followed by an additional 1:1 wash and size selection with HXB. HXB is equal parts 40% PEG8000 (Fisher FIBBP233) and 5M NaCl. The anti-CTCF antibody is Active Motif 61311, and the anti-HOXD13 antibody is Abcam Ab19866.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CUT&RUN
|
| Data processing |
Library strategy: CUT&RUN
CUT and RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 1000 –fr –dovetail –very-sensitive).
Reads with mapping quality below 30 or not properly paired were removed from the analysis. PCR duplicates were removed.
The output BAM file was converted to BED using bamtobed bedtools v2.18.2 (Quinlan, 2014).
The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008) (--format BED --keep-dup all --bdg --nomodel --extsize 200 --shift 100).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage from macs2
narrowPeak: narrowPeak from macs2
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jul 20, 2021 |
| 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) |
| GSE165492 |
Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [CUT&RUN] |
| GSE165495 |
Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations |
|
| Relations |
| BioSample |
SAMN17545769 |
| SRA |
SRX9934252 |
