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Sample GSM4542765 Query DataSets for GSM4542765
Status Public on Oct 26, 2021
Title WT_D4_normalBMP4_Rep1_ATAC-seq
Sample type SRA
 
Source name WT_D4_normalBMP4
Organism Mus musculus
Characteristics cell type: mouse ES cell derived cardiac mesoderm
genotype: Brg1-3xFLAG
timepoint: Day 4
Treatment protocol ES cells were differentiated to cardiac precursor or cardiomyocytes before harvested for ATACseq
Growth protocol Es cell were differentiated following Katman et al., 2011 and Wamstad et al., 2012 papers
Extracted molecule genomic DNA
Extraction protocol We followed Corces et al., 2017 paper to perform ATACSeq
Lysed nuclei were tagmented at 37C for 45 mins for D4, and D6 samples and 3hrs for D10 samples, before purified and PCR amplified with Ad1 and Ad2 primers (corces et al., 2017)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Libraries were sequenced on Nextseq 500
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9 using the bowtie
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
 
Submission date May 09, 2020
Last update date Oct 26, 2021
Contact name Benoit Bruneau
E-mail(s) benoit.bruneau@gladstone.ucsf.edu
Organization name Gladstone Institute of Cardiovascular Disease
Street address 1650 Owens Street
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL19057
Series (2)
GSE150180 ATACseq of WT and BRM KO cells at D4, D6 and D10 of cardiac differentiation
GSE150186 Brahma safeguards canalization of cardiac mesoderm differentiation
Relations
BioSample SAMN14860202
SRA SRX8297686

Supplementary file Size Download File type/resource
GSM4542765_Average_WT_D4_normalBMP4.bw 121.5 Mb (ftp)(http) BW
GSM4542765_WT_D4_normalBMP4_Rep1.bw 454.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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