EXPERIMENT_TITLE: GSM3909728: R3: released 3.5 hours; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For each Hi-C library, approximately 5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation Hi-C was performed according to published protocol (Belagzhal et al., 2017)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: DpnII Hi-C libraries for samples synchronized to G2/M using single 24h thymidine, 3h release, and 12h nocodazole--these samples are then released for x amount of time Overall design: Hi-C
SAMPLE_TITLE: R3: released 3.5 hours
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HeLa-S3 cells"}, {"TAG": "protocol", "VALUE": "Hi-C"}, {"TAG": "enzyme", "VALUE": "DpnII"}, {"TAG": "cell line", "VALUE": "Human adenocarcinoma cells"}]
Pool_Member_@attributes_sample_title: R3: released 3.5 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R3: released 3.5 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R3-T35-R3-T1_S19_L007_R1_001.fastq.gz", "size": "2914676928", "date": "2019-06-28 01:19:08", "md5": "02161c248a830dc49f47f59b678f0688", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R3-T35-R3-T1_S19_L007_R2_001.fastq.gz", "size": "3073311678", "date": "2019-06-28 01:18:08", "md5": "05a0bed54ee207ef99a0604ae336448e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609701", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609701/SRR9609701", "size": "3498670803", "date": "2019-06-28 01:20:30", "md5": "6d9484ce78edb51ada2a457c437e4be1", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609701.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR009/609/SRR9609701.sralite.1", "size": "2401295187", "date": "2020-06-22 08:50:28", "md5": "19df275b981fac923e2888ac1ddbaca2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]