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Sample GSM7385433 Query DataSets for GSM7385433
Status Public on Jun 01, 2024
Title ATAC_H_E115-WT_rep2
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 SAMN35178266
SRA SRX20437306

Supplementary file Size Download File type/resource
GSM7385433_LPMO_062317_1H_h_02_ATAC.bw.gz 200.0 Mb (ftp)(http) BW
GSM7385433_LPMO_062317_1H_h_02_ATAC.narrowPeak.gz 1.9 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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