EXPERIMENT_TITLE: GSM3909715: R2: 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: R2: 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: R2: released 3.5 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R2: released 3.5 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-T35_S9_L003_R1_001.fastq.gz", "size": "4034098067", "date": "2019-06-28 01:26:52", "md5": "0cb8ce7a0a4b53b97cc08d0452e74b0f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-T35_S9_L003_R2_001.fastq.gz", "size": "4403311715", "date": "2019-06-28 01:28:15", "md5": "57aa298c572c5a222b14f455e434ff08", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609688", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609688/SRR9609688", "size": "4984444147", "date": "2019-06-28 01:30:26", "md5": "1f556e9c36c194d6147681af2d72f767", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609688.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/609/SRR9609688.sralite.1", "size": "3297794595", "date": "2020-06-19 22:09:02", "md5": "cfacb41e5fdf326f7e81e7165844dd60", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]