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Sample GSM3263052 Query DataSets for GSM3263052
Status Public on Jul 09, 2019
Title day00.Input.Batch1.Rep1
Sample type SRA
 
Source name Embryonic stem cell
Organism Homo sapiens
Characteristics tissue: Embryonic stem cell
differentiation time: day00
genotype: H9 MLC2v:H2B
matched input: N/A
chip antibody: none (input)
Extracted molecule genomic DNA
Extraction protocol ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441). Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf, Library preparation: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq and Hi-C, rnaSTAR for RNA-seq. Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with juicebox.jar provided by Aiden lab).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for ChIP-seq and input, juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) for RNA-seq.
 
Submission date Jul 10, 2018
Last update date Oct 22, 2024
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
ZIP/Postal code 92093
Country USA
 
Platform ID GPL20301
Series (2)
GSE116862 Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries.
GSE186958 Chromatin structure dynamics during human cardiomyocyte differention
Relations
BioSample SAMN09637474
SRA SRX4377111

Supplementary file Size Download File type/resource
GSM3263052_Input_D0_1_AY2439.filt.nodup.srt.bw 564.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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