EXPERIMENT_TITLE: GSM3741968: Hi-C_48hr_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_48hr_6bp_Rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "48 hours"}, {"TAG": "replicate", "VALUE": "1"}]
Pool_Member_@attributes_sample_title: Hi-C_48hr_6bp_Rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_48hr_6bp_Rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994263.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR008/994/SRR8994263.sralite.1", "size": "2607289904", "date": "2020-06-20 12:57:32", "md5": "17d888a671a8301be9104afd5f8f56f2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994263", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994263/SRR8994263", "size": "3828999304", "date": "2019-05-01 09:39:04", "md5": "f17f8f145ff882ceec4f854448f65c76", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_48hr_6bp_Rep1_Read2.fastq.gz", "size": "3204069182", "date": "2020-01-18 12:54:35", "md5": "d1d41d7e6144c9f1c73f050e53c8c15e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_48hr_6bp_Rep1_Read1.fastq.gz", "size": "3184386283", "date": "2020-01-18 13:09:20", "md5": "bb8ef806a37a132306d52e9c038b8ad3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]