EXPERIMENT_TITLE: GSM3909688: R1: released 6 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: R1: released 6 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: R1: released 6 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R1: released 6 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609661.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/609/SRR9609661.sralite.1", "size": "2356387634", "date": "2020-06-19 21:48:33", "md5": "5ce498361b76bcc4538a540771308ff9", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609661", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609661/SRR9609661", "size": "3148546582", "date": "2019-06-28 01:22:14", "md5": "a22730f06a9b59848b606101ce911138", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T6_S18_L007_R2_001.fastq.gz", "size": "2755219355", "date": "2019-06-28 01:18:30", "md5": "7bea0f32bc6bdd31daa6168b8a1b4f23", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T6_S18_L007_R1_001.fastq.gz", "size": "2736751108", "date": "2019-06-28 01:16:28", "md5": "9be32e93fa46677620c85910839c2d43", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]