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SRX1157718: ChIP-Seq input analysis of peripheral mononuclear cell from TC015 (A21632)
1 ILLUMINA (Illumina HiSeq 2000) run: 29.1M spots, 2.2G bases, 1.3Gb downloads

Design: ChIP-Seq input analysis of peripheral mononuclear cell from TC015 (A21632) using Illumina HiSeq 2000
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 Blood of a human male participant in the dbGaP study "Integrated Epigenetic Maps of Human Embryonic, Extraembryonic and Adult Cells"
SAMN03416872 • SRS1039145 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: A21632
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: RANDOM
Layout: SINGLE
Construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
Experiment attributes: (show all 7 attributes...) (hide...)
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation ( (show full text...)(hide...)
Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 94-294 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: 1 run, 29.1M spots, 2.2G bases, 1.3Gb
Run# of Spots# of BasesSizePublished
SRR217268729,092,4572.2G1.3Gb2016-03-25

ID:
1682947

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