EXPERIMENT_TITLE: GSM3909703: R1: G2/M sample (t = 0 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: G2/M sample (t = 0 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: G2/M sample (t = 0 hours)
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R1: G2/M sample (t = 0 hours)
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T0_S3_L002_R1_001.fastq.gz", "size": "2286615677", "date": "2019-06-28 01:09:22", "md5": "caf25bfd445fce20a58d0a810459a855", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T0_S3_L002_R2_001.fastq.gz", "size": "2364030554", "date": "2019-06-28 01:08:41", "md5": "d3466af6da150b8423548ea47bb97eca", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609676", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609676/SRR9609676", "size": "2677497313", "date": "2019-06-28 01:10:26", "md5": "7491463db733bcd39c548aaa7f44ec26", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609676.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/609/SRR9609676.sralite.1", "size": "1923574213", "date": "2020-06-20 07:34:02", "md5": "49ca0cbda6c17541440df7df4dd87677", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]