EXPERIMENT_TITLE: GSM3741967: Hi-C_24hr_6bp_Rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C libraries were created using HindIII 6bp restriction enzyme based on Dixon et al., 2015 protocol or using DpnII 4bp restriction enzyme based on Rao et al., 2014 in-situ Hi-C protocol Final libraries were sequenced by Hudosn Alpha Sequencing facility on Illumina-HiSeq 2500
STUDY_DESCRIPTOR_STUDY_ABSTRACT: This study demonstrates the relationship between replication timing, transcription and chromatin compartments in human stem cell differenatiation to endoderm lineage (Hi-C). Overall design: Measuring replication timing, transcription and chromatin organization using Hi-C at different time points during human stem cell differentiation to endoderm lineage.
SAMPLE_TITLE: Hi-C_24hr_6bp_Rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "24 hours"}, {"TAG": "replicate", "VALUE": "2"}]
Pool_Member_@attributes_sample_title: Hi-C_24hr_6bp_Rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_24hr_6bp_Rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994262", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994262/SRR8994262", "size": "3688591903", "date": "2019-05-01 09:34:27", "md5": "d553f4433c79a8f19ef5231c7183bb0b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994262.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR008/994/SRR8994262.sralite.1", "size": "2499390787", "date": "2020-06-19 23:53:34", "md5": "fa3980872eb5b302a3adf5b67cbee559", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_24hr_6bp_Rep2_Read2.fastq.gz", "size": "3108770548", "date": "2020-01-18 13:41:54", "md5": "0408fd65c682f0be81ae25a28d685fe9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_24hr_6bp_Rep2_Read1.fastq.gz", "size": "3045783258", "date": "2020-01-18 12:52:32", "md5": "bb4368c8c7b59d56653b9758ad709314", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]