EXPERIMENT_TITLE: GSM3741965: Hi-C_H9_ESC_6bp; 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_6bp
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human ESC (H9)"}, {"TAG": "differentiation state", "VALUE": "ESC"}, {"TAG": "replicate", "VALUE": "2"}]
Pool_Member_@attributes_sample_title: Hi-C_H9_ESC_6bp
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_H9_ESC_6bp
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8994260.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR008/994/SRR8994260.sralite.1", "size": "3675154731", "date": "2020-06-20 18:10:56", "md5": "d1e89bbdf9b72ddf5c89095bddc1f2db", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8994260", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8994260/SRR8994260", "size": "5719930983", "date": "2019-05-01 10:00:26", "md5": "fe07cb76fe73d2dc17751809b794bbd0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_H9_ESC_6bp_Read2.fastq.gz", "size": "4770411493", "date": "2020-01-18 13:55:04", "md5": "3956f92c40a68b7eb3b7c06076c85e2c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_H9_ESC_6bp_Read1.fastq.gz", "size": "4663524990", "date": "2020-01-18 13:56:15", "md5": "5df6c4801d7d05574cfeedd645009731", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]