EXPERIMENT_TITLE: GSM3741969: Hi-C_48hr_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_48hr_6bp_Rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "48 hours"}, {"TAG": "replicate", "VALUE": "2"}]
Pool_Member_@attributes_sample_title: Hi-C_48hr_6bp_Rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_48hr_6bp_Rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994264.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR008/994/SRR8994264.sralite.1", "size": "1818602919", "date": "2020-06-20 01:40:56", "md5": "68aa3f7808ed014eed02be51feef4909", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994264", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994264/SRR8994264", "size": "2692186515", "date": "2019-05-01 09:21:43", "md5": "e9c50f694db55f0f5122743d3121bcb7", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_48hr_6bp_Rep2_Read2.fastq.gz", "size": "2282842874", "date": "2020-01-18 13:02:40", "md5": "3b17250708db95e11f6261307927ab96", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_48hr_6bp_Rep2_Read1.fastq.gz", "size": "2227954623", "date": "2020-01-18 13:26:42", "md5": "98419038e49c77e8cba4df552924b782", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]