EXPERIMENT_TITLE: GSM3909717: R2: released 2.5 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 2.5 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 2.5 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R2: released 2.5 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-T25_S7_L002_R1_001.fastq.gz", "size": "3408566569", "date": "2019-06-28 01:20:57", "md5": "75a5cb3e62c7a5fdff26c3a4727a1385", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-T25_S7_L002_R2_001.fastq.gz", "size": "3641053747", "date": "2019-06-28 01:22:32", "md5": "7b3addee6a739dcb2f0d53234581efd0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609690", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609690/SRR9609690", "size": "4153250637", "date": "2019-06-28 01:24:41", "md5": "98531fb2b46e7f3ff06b611df4712053", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609690.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/609/SRR9609690.sralite.1", "size": "2727625193", "date": "2020-06-21 05:48:59", "md5": "6ff37b39f765da12f6f8b06f6719bb28", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]