EXPERIMENT_TITLE: GSM3741964: Hi-C_H9_ESC_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_H9_ESC_4bp
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "ESC"}, {"TAG": "replicate", "VALUE": "1"}]
Pool_Member_@attributes_sample_title: Hi-C_H9_ESC_4bp
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_H9_ESC_4bp
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994259", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994259/SRR8994259", "size": "7759579768", "date": "2019-05-01 10:54:33", "md5": "9f98f2b17c4003532dd9f72df7c04e79", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994259.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR008/994/SRR8994259.sralite.1", "size": "6449956572", "date": "2020-06-23 05:17:07", "md5": "7dace3bcb9571940f19b75f8a3381845", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_H9_ESC_4bp_Read2.fastq.gz", "size": "6850785267", "date": "2020-01-18 12:13:57", "md5": "e513344a7e5bfb669e563470b2d68ab6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_H9_ESC_4bp_Read1.fastq.gz", "size": "6643555749", "date": "2020-01-18 11:15:04", "md5": "fd112c779891c071803dc2cce16fa743", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]