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Status |
Public on Jul 09, 2019 |
Title |
day00.Input.Batch1.Rep1 |
Sample type |
SRA |
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Source name |
Embryonic stem cell
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Organism |
Homo sapiens |
Characteristics |
tissue: Embryonic stem cell differentiation time: day00 genotype: H9 MLC2v:H2B matched input: N/A chip antibody: none (input)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 4000 |
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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.
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Submission date |
Jul 10, 2018 |
Last update date |
Oct 22, 2024 |
Contact name |
Bing Ren |
E-mail(s) |
biren@ucsd.edu
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Organization name |
University of California, San Diego
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Street address |
9500 Gilman Drive
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City |
La Jolla |
ZIP/Postal code |
92093 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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