|
| Status |
Public on Jun 01, 2024 |
| Title |
ATAC_H_E115-WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
embryonic day: E11.5
genotype: WT
tissue: mouse embryonic heart
|
| Growth protocol |
Pairs of embryonic hearts of wildtype embryos at E11.5 (49-51 somite-stage) were microdissected in cold PBS and subjected to tissue dissociation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were dissociated in Lysis buffer using a Dounce tissue grinder and approx. 50000 cells were pelleted and resuspendend in 50uL transposition reaction mix.
Samples were incubated in transposition reaction mix (25 μL Nextera 2x TD buffer and 2.5 μL TDE1; Illumina) for 30 minutes at 37C with shaking. Following amplification, ATAC-libraries were purified, quantified and quality assessed using a Agilent Bioanalyzer. Libraries were pooled and sequences on an Illumina HiSeq 4000 (single end 50bp).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Tn5-tagmentation of open chromatin regions
|
| Data processing |
ATAC-seq datasets were subjected to adaptor trimming (trim_galore_v0.6.6) by Cutadapt with default parameters ‘-j 1 -e 0.1 -q 20 -O 1’ for single-end. Bowtie2 (version 2.4.2) was used for read mapping with parameters ‘-q --no-unal -p 8 -X2000’. Reads were aligned to the GRCm38/mm10 reference genome using pre-built Bowtie2 indexes from the Illumina’s iGenomes collection (http://bowtie-bio.sourceforge.net/bowtie2/). Duplicates and low-quality reads (MAPQ = 255) were removed using SAMtools (v1.12), with pipeline parameters ‘markdup -r’ and ‘-bh -q10’, respectively. Peak calling was performed using MACSv2 (v2.1.0) with p-value < 0.01 and parameters ‘-t -n -f BAM -g mm --nolambda --nomodel --shif 50 --extsize 100’.
Assembly: GRCm38/mm10
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Marco Osterwalder |
| E-mail(s) |
olheartdev@gmail.com
|
| Organization name |
Universiy of Bern
|
| Department |
DBMR
|
| Lab |
Osterwalder Lab
|
| Street address |
Murtenstrasse 24
|
| City |
Bern |
| ZIP/Postal code |
3008 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE232882 |
A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [ATAC-seq] |
| GSE232887 |
A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival |
|
| Relations |
| BioSample |
SAMN35178267 |
| SRA |
SRX20437305 |
