EXPERIMENT_TITLE: Illumina HiSeq 2000 sequencing; Exploiting native forces to capture chromosome conformation in mammalian cell nuclei
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were treated with 10 ng/ml TNFalpha for 60 min where indicated Libraries were generated by inverse PCR using primers already carrying Illumina adapter sequences and targeting the TSSs of the genes indicated
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Here, we developed a novel chromosome conformation capture (3C) method for capturing the 3D spatial contacts of endogenous genomic loci without a need for crosslinking. This method, i3C, was applied to multiple loci in two different human primary (ENCODE) cell lines, HUVEC and IMR90, and in the absence or presence of a proinflammatory stimulus (TNFalpha). Coupled to high throughput sequencing on an Illumina HiSeq200 platform, i3C generated aprrox. 8 million single-end reads per experiment.
SAMPLE_TITLE: Native_HiC_rep2_2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA first public", "VALUE": "2016-12-12"}, {"TAG": "ENA last update", "VALUE": "2016-12-06"}, {"TAG": "External Id", "VALUE": "SAMEA21230668"}, {"TAG": "INSDC center alias", "VALUE": "University of Cologne, Germany"}, {"TAG": "INSDC center name", "VALUE": "University of Cologne, Germany"}, {"TAG": "INSDC first public", "VALUE": "2016-12-12T11:05:38Z"}, {"TAG": "INSDC last update", "VALUE": "2016-12-06T16:44:11Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "E-MTAB-47191481038065:Native_HiC_rep2_2"}, {"TAG": "broker name", "VALUE": "ArrayExpress"}, {"TAG": "cell line", "VALUE": "HUVEC"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "endonuclease for library preparation", "VALUE": "DPNII"}, {"TAG": "sample name", "VALUE": "E-MTAB-47191481038065:Native_HiC_rep2_2"}]
Pool_Member_@attributes_sample_title: Native_HiC_rep2_2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Native_HiC_rep2_2
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