EXPERIMENT_TITLE: GSM3909694: R1: released 3 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 3 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 3 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R1: released 3 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T3_S12_L005_R1_001.fastq.gz", "size": "2917424582", "date": "2019-06-28 01:30:35", "md5": "47d4b299019c6f4a119de8b2fbcb9c56", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T3_S12_L005_R2_001.fastq.gz", "size": "2949204555", "date": "2019-06-28 01:28:48", "md5": "ceddb80e8feb8a4ee0972d51b2c7204a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609667", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609667/SRR9609667", "size": "3379694439", "date": "2019-06-28 01:37:23", "md5": "9575555c1c3fb60cfe21af607854a854", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609667.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR009/609/SRR9609667.sralite.1", "size": "2500087815", "date": "2020-06-22 08:47:41", "md5": "9f3f8cd3e8b4618f740c8e3471f0ded7", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]