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SRX010885: MRE-Seq analysis of H1 embryonic stem cell line (HS1153)
4 ILLUMINA (Illumina Genome Analyzer II) runs: 53.7M spots, 4.1G bases, 2.3Gb downloads

Design: MRE-Seq analysis of H1 embryonic stem cell line (HS1153) using Illumina Genome Analyzer IIx
Submitted by: BC Cancer Agency Michael Smith Genome Sciences Centre (BCCAGSC)
Study: Roadmap Epigenomics Program - UCSF
show Abstracthide Abstract
We propose to work cooperatively with other Mapping Centers and the Data Coordination Center (EDACC) funded by this Roadmap mechanism to comprehensively map epigenomes of select human cells with significant relevance to complex human disease. Our group, consisting of scientists at UCSF, UC Davis, UCSC and the British Columbia Genome Sciences Centre has the broad expertise that this project requires. We will focus on cells relevant to human health and complex disease including cells from the blood, brain, breast and U.S. Government-approved lines of human embryonic stem cells (aim 1). We will incorporate high quality, homogeneous cells from males and females, and two predominant racial groups, and biological replicates of each cell type. Production of comprehensive maps will include 6 histone modifications selected for their opposing roles in regulating active and inactive chromatin (aim 2), DNA methylation (aim 3) and miRNA and gene expression (aim 4)... (for more see dbGaP study page.)
Sample: Non-tumor DNA sample from Embryo ICM of a human male participant in the dbGaP study "Integrated Epigenetic Maps of Human Embryonic, Extraembryonic and Adult Cells"
SAMN03416742 • SRS1249016 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: HS1153
Instrument: Illumina Genome Analyzer II
Strategy: MRE-Seq
Source: GENOMIC
Selection: Restriction Digest
Layout: SINGLE
Construction protocol: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
Experiment attributes: (show all 5 attributes...) (hide...)
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construc (show full text...)(hide...)
Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
The SRA run(s) below contain human sequence (more...)(less...)

These data are available through the dbGaP authorized access system. Request access to:

  • Study:  phs000791
  • Consent Group: HMB

Runs: 4 runs, 53.7M spots, 4.1G bases, 2.3Gb
Run# of Spots# of BasesSizePublished
SRR0266598,889,594675.6M359.1Mb2016-03-25
SRR02666014,699,9211.1G672.6Mb2016-03-25
SRR02666114,780,2031.1G654.3Mb2016-03-25
SRR02666215,343,8661.2G658Mb2016-03-25

ID:
11172

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