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Sample GSM5670289 Query DataSets for GSM5670289
Status Public on Jun 30, 2023
Title H1-D1-ATF4
Sample type SRA
Source name human embryonic stem cells
Organism Homo sapiens
Characteristics cell line: H1
cell type: human embryonic stem cells (hESCs)
treatment: untreated
differentiation time: Day1
chip antibody: ATF4 (CST, 11815)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. ChIP-seq libraries were generated and sequenced an Illumina HiSeq X Ten with 150 bp paired-end reads by Novogene.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
Data processing Illumina Casava software used for basecalling.
Raw ChIP-seq sequenced reads were trimmed for adapters and low sequencing quality bases using fastp
BWA was used to map the 150 bp paired-end reads to the GRCh38/hg38 Homo sapiens reference genome
Mark duplicates by Picard and remove duplicates.
The SPP program was used to call peaks, and an IDR-based strategy was used to identify stable peaks across pseudo-replicates.
Genome_build: hg38
Supplementary_files_format_and_content: peak text file
Submission date Nov 04, 2021
Last update date Jun 30, 2023
Contact name Weisheng Cheng
Organization name Sun yat-sen University
Street address 2nd Zhongshan Road
City Guangzhou
ZIP/Postal code 510080
Country China
Platform ID GPL20795
Series (2)
GSE188112 Chromatin occupancy of ATF4 at day 1 of cardiomyocytes differentiation [ChIP-seq]
GSE188123 RNA-seq and ChIP-seq studies of cardiomyocyte differentiation from H1 hESCs
BioSample SAMN22876525
SRA SRX12969424

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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