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Sample GSM2991263 Query DataSets for GSM2991263
Status Public on May 02, 2019
Title E8_75_control_ATAC-seq_Rep1
Sample type SRA
 
Source name E 8.75 mouse embryos
Organism Mus musculus
Characteristics genotype: wt
Extracted molecule genomic DNA
Extraction protocol Pharyngeal mesoderm and hearts were dissected from E8.75 embryos (6 somites stage). Tissues were resuspended in 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) and used for ATAC Library preparation using Tn5 Transposase from Nextera DNA Library Prep Kit (Illumina #15028211). After centrifugation (10 min, 500 g at 4 °C), cell pellet was resuspended in transposition reaction mix (25 µl TD-Buffer, 2.5 µl Tn5, 22.5 µl water) and incubated for 30 min at 37 °C with gentle mixing. Immediately following the transposition reaction, purification was carried out using MinElute PCR Purification Kit (Qiagen #28004).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description E8_75_control_ATAC-seq.bw
E8_75_control_ATAC-seq_peaks_annot.txt
Data processing ATAC-Seq reads were mapped with bowtie2 to mm9 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads.
The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks calling was performed with MACS14 (p1e5 –nomodel and –shiftsize 100), and peaks overlapping blacklist defined by ENCODE with the help of Bedtools v2.15 (intersect -wa).
Bedtools v2.15 (intersect -wa) was used to obtain open chromatin regions overlapping by at least 1 bp in the replicates.
BamCoverage function of deepTools2 (-b 20 -smooth 40 -e 150) was used to create normalized bigwig files (reads per genome coverage, RPGC). Further, bigWigAverageOverBed (https://github.com/ENCODE-DCC/kentUtils) was used to quantify mapped reads on peaks areas.
Heatmap and densitity plots were created using computeMatrix followed by plotHeatmap or plotProfile from deepTools2. To permit a comparative display of data within a deeptools profile heatmap, size factors produced by edgeR based on unified peak counts were used to scale samples to account for differences in sequencing depth, library composition, and ATAC-Seq efficiency.
Genome_build: mm9
Supplementary_files_format_and_content: Bw
 
Submission date Feb 09, 2018
Last update date May 03, 2019
Contact name Gergana Dobreva
E-mail(s) Gergana.Dobreva@medma.uni-heidelberg.de
Organization name Medical Faculty Mannheim/University of Heidelberg
Department Cardiovascular Genomics and Epigenomics
Lab AG Dobreva
Street address Ludolf-Krehl-Str. 7-11
City Mannheim
State/province Baden Württemberg
ZIP/Postal code 68167
Country Germany
 
Platform ID GPL17021
Series (2)
GSE80383 Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
GSE110436 Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [E8.75_Embryo_ATAC-seq]
Relations
BioSample SAMN08514518
SRA SRX3678597

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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