EXPERIMENT_TITLE: Human LV HiChIP
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The Activity-by-contact algorithm 3 tackles this issue by multiplying measures of enhancer activity and enhancer-promoter 3D contacts, and thence predicts a weighted enhancer-gene connections in a given cell type based on chromatin state map. Different enhancer loci corresponding to a gene are scored, scores greater than 0.05 are predicted to have a regulatory effect on the target genes, and higher scores indicate stronger contribution to the gene. Evidence suggests that ABC outperforms other models of predicting target genes of enhancers including H3K27ac HiChIP, RNA PolII ChIA-PET, TargetFinder, and others. Hence, to annotate and prioritise a global catalogue of cardiac disease-causing gene enhancers, we applied ABC algorithm to datasets of human whole left ventricles.
SAMPLE_TITLE: LV_HiChIP_2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "LV donor 2"}, {"TAG": "age", "VALUE": "50"}, {"TAG": "biomaterial_provider", "VALUE": "Genome Institute of Singapore"}, {"TAG": "sex", "VALUE": "male"}, {"TAG": "tissue", "VALUE": "left ventricle"}, {"TAG": "disease", "VALUE": "Non-failing"}, {"TAG": "disease_stage", "VALUE": "Non-failing"}, {"TAG": "ethnicity", "VALUE": "European"}, {"TAG": "sample_type", "VALUE": "tissue"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: LV_HiChIP_2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LV_HiChIP_2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_1.fastq.gz", "size": "4622454500", "date": "2020-03-23 09:11:33", "md5": "2b703b99cdfed79261acdacaccb9f75e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_10.fastq.gz", "size": "5077423447", "date": "2020-03-23 09:56:08", "md5": "73d554babaf6ae54be748aabdeef929e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_11.fastq.gz", "size": "4943518413", "date": "2020-03-23 09:58:17", "md5": "d6fdb4b6d27b474bfd08c609ba761ee9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_12.fastq.gz", "size": "5036581923", "date": "2020-03-23 10:00:25", "md5": "7591a9e8d6469f308a3fbaa7b223c123", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_13.fastq.gz", "size": "4592222254", "date": "2020-03-23 09:53:19", "md5": "e01009ffe2ac729346a459f8f2ad4d2e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_14.fastq.gz", "size": "4716431271", "date": "2020-03-23 09:14:12", "md5": "a55fd4bf78b7fe9e514643de29bd421c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_15.fastq.gz", "size": "4540451951", "date": "2020-03-23 09:09:38", "md5": "535587c7ca924deecad4d3130f56d5bf", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_16.fastq.gz", "size": "2914224078", "date": "2020-03-23 09:03:10", "md5": "2167ac950da543dca2af6d7be44d0581", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_2.fastq.gz", "size": "4743927440", "date": "2020-03-23 09:50:40", "md5": "e68ce3580fdf5bb24567ad1656ec789e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_3.fastq.gz", "size": "4586311932", "date": "2020-03-23 09:06:25", "md5": "b6abc3fda9aea2b514ee7cc28ef1e8a0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_4.fastq.gz", "size": "4670800985", "date": "2020-03-23 09:07:54", "md5": "d2457129328d3dea13b426b7468a3eaa", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_5.fastq.gz", "size": "4174460593", "date": "2020-03-23 09:16:23", "md5": "a0a072e3d31206a5170d784605cffc2a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_6.fastq.gz", "size": "4517070033", "date": "2020-03-23 09:29:44", "md5": "271f2d8d5dbabcd1c748b191037a87f0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_7.fastq.gz", "size": "4207532737", "date": "2020-03-23 09:47:44", "md5": "332a93f7b434f7bbbe1774f07f8b4756", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_8.fastq.gz", "size": "3995190380", "date": "2020-03-23 09:33:57", "md5": "c47fb6f481a2d1e4eb58dcec3d986bd2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read2_9.fastq.gz", "size": "4896975189", "date": "2020-03-23 09:20:57", "md5": "981a11d87de52bef34c43736b877056a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR11365445", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11365445/SRR11365445", "size": "96642961814", "date": "2020-03-23 12:07:08", "md5": "309317441e4ff9a1351b8b5dfc355270", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_9.fastq.gz", "size": "3872257562", "date": "2020-03-23 09:37:45", "md5": "213f26a010b2d608a06ca41a70435674", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_8.fastq.gz", "size": "3149952860", "date": "2020-03-23 09:05:13", "md5": "812025dec9bddb162bdd1144a2735517", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_7.fastq.gz", "size": "3610438028", "date": "2020-03-23 09:35:46", "md5": "c62acfbf5fb682f5b6ac6ad68a0b5850", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_6.fastq.gz", "size": "3620254743", "date": "2020-03-23 09:02:10", "md5": "2903364f6443ebb3a7ef98a37246cc2d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_5.fastq.gz", "size": "3607455959", "date": "2020-03-23 08:59:29", "md5": "a448bffeaf42a2d6c181db0111b008b9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_4.fastq.gz", "size": "3661418891", "date": "2020-03-23 09:27:21", "md5": "9c94663209e84df8b8e21ef36eed984a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_3.fastq.gz", "size": "3680234954", "date": "2020-03-23 09:32:17", "md5": "c8fb9787c44215b3116e011e4560a063", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_2.fastq.gz", "size": "3628866139", "date": "2020-03-23 09:00:57", "md5": "0997c98ddb6f690cf66bc7392480982a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_16.fastq.gz", "size": "2299554028", "date": "2020-03-23 08:58:15", "md5": "515453c7de05497d111b810b990209af", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_15.fastq.gz", "size": "3753923529", "date": "2020-03-23 09:18:24", "md5": "ca80d9d44298827c6da8186f003e9fb5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_14.fastq.gz", "size": "3749424305", "date": "2020-03-23 09:03:59", "md5": "c6db8daa858021a7030167d9c1ab153d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_13.fastq.gz", "size": "3805798785", "date": "2020-03-23 09:45:20", "md5": "74698413d5079e922d4f221acfbbbc08", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_12.fastq.gz", "size": "3835420350", "date": "2020-03-23 09:42:51", "md5": "23fe4f5225c42ef1859150ee9ee998a8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_11.fastq.gz", "size": "3858265611", "date": "2020-03-23 09:40:13", "md5": "4a7215f455082f21c240ae60a025be77", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_10.fastq.gz", "size": "3886265112", "date": "2020-03-23 09:23:46", "md5": "8f871b08079f5d9820431f57c95104c5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CHH49170_Rep1_read1_1.fastq.gz", "size": "3651504352", "date": "2020-03-23 09:13:06", "md5": "f9e13c47fe6191caf103fbca4103ac93", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR11365445.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR011/11365/SRR11365445/SRR11365445.lite.1", "size": "58551018062", "date": "2022-07-27 10:53:37", "md5": "65391e75b9893aaec84cb61bab3b9290", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]