EXPERIMENT_TITLE: GSM3741970: Hi-C_Definitve Endoderm_4bp; 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_Definitve Endoderm_4bp
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "Definitive Endoderm"}, {"TAG": "replicate", "VALUE": "1"}]
Pool_Member_@attributes_sample_title: Hi-C_Definitve Endoderm_4bp
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_Definitve Endoderm_4bp
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994265.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR008/994/SRR8994265.sralite.1", "size": "15803956537", "date": "2020-06-20 04:45:29", "md5": "0eaa35a23bb35689eb7ddde5902cf040", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994265", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994265/SRR8994265", "size": "18861153013", "date": "2019-05-01 12:56:13", "md5": "09acb85e2e1e191f6558e42466c91c98", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_Definitive_Endoderm_4bp_Read2.fastq.gz", "size": "16378664963", "date": "2020-01-18 12:27:36", "md5": "b820e616c915642b51836e6e64bd7c16", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_Definitive_Endoderm_4bp_Read1.fastq.gz", "size": "16307154686", "date": "2020-01-18 12:19:00", "md5": "7fec8a74bbd53e3b5adb58c89cb25b91", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]