EXPERIMENT_TITLE: GSM3741966: Hi-C_24hr_6bp_Rep1; 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_Rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "24 hours"}, {"TAG": "replicate", "VALUE": "1"}]
Pool_Member_@attributes_sample_title: Hi-C_24hr_6bp_Rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_24hr_6bp_Rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994261", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994261/SRR8994261", "size": "1552571753", "date": "2019-05-01 09:14:15", "md5": "1f25e75241a491c4b2470df43f6b54b8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_24hr_6bp_Rep1_Read2.fastq.gz", "size": "1305125309", "date": "2020-01-18 12:54:03", "md5": "de41132ead5e9a2dac707e85abcbb519", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_24hr_6bp_Rep1_Read1.fastq.gz", "size": "1287616267", "date": "2020-01-18 13:22:05", "md5": "cc3b7e0472bf90b882743f119db09be1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994261.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR008/994/SRR8994261.sralite.1", "size": "1004865497", "date": "2020-06-23 04:15:26", "md5": "c4b5c6fb613639211a93c9b133196a6e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]