NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3262992 Query DataSets for GSM3262992
Status Public on Jul 09, 2019
Title day00.H3K27ac.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: day00.Input.Batch1.Rep1
chip antibody: H3K27ac
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 SAMN09637462
SRA SRX4377051

Supplementary file Size Download File type/resource
GSM3262992_H3K27ac_D0_1_AY2463.filt.nodup.srt.bw 200.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap