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Sample GSM3637969 Query DataSets for GSM3637969
Status Public on Jun 22, 2019
Title flbioNkx2-5_E8.75_SHF_input
Sample type SRA
 
Source name heart
Organism Mus musculus
Characteristics genotype/variation: NKX2.5fb/+::BirA/BirA
developmental stage: E8.75
tissue: Heart
heart field: Second
chip antibody: None
Growth protocol Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory take care.
Extracted molecule genomic DNA
Extraction protocol Cells were lysed at 37°C before chromatin was fragmented, adaptor-ligated and released. For one bio-ChIP experiment, 10 μl streptavidin beads (Invitrogen, cat#60210) were used for incubation for 2 h at 4°C. Beads were briefly washed with 2% SDS/PBS once, and then washed with high salt buffer (1% Triton X-100, 2 mM EDTA, 50 mM HEPES pH 7.9, 500 mM NaCl, 0.1% sodium deoxycholate) for three times. Beads were re-suspended in 100 μl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After reverse crosslinking and proteinase K digestion, DNA was purified through phenol-chloroform extraction.
NEBNext Ultra II Master Mix was used for PCR enrichment, followed by size selection of 200-800 bp. The resulting libraries were subjected to 2 X 150 bp paired-end sequencing on NovaSeq 6000 systems.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description Input DNA
Data processing Basecalls performed using CASAVA version 1.8.2.
ChIP-seq reads were filtered by cutadapt (v1.11) with parameters to get high quality reads.
High-quality reads were aligned to mm10 mouse genome using bowtie2 (v2.3.1) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 30 were kept.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files that represented ChIP signals were generated using deeptools.
 
Submission date Mar 01, 2019
Last update date Jun 22, 2019
Contact name Haiqing Xiong
E-mail(s) haiqingxiong@pku.edu.cn
Organization name Peking University
Street address 5 Yiheyuan Road, Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL24247
Series (2)
GSE108961 Single-cell transcriptomics reveals chemotaxis mediated intra-organ crosstalk during cardiogenesis [ChIP-seq]
GSE108963 Single-cell transcriptomic analysis reveals lineage hierarcies and communications for second heart lineage deployment
Relations
BioSample SAMN11042492
SRA SRX5453248

Supplementary file Size Download File type/resource
GSM3637969_flbioNkx2-5_E8.75_SHF_input.bw 419.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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