EXPERIMENT_TITLE: GSM3909698: R1: released 2 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 2 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 2 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R1: released 2 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T2_S8_L003_R1_001.fastq.gz", "size": "2632284035", "date": "2019-06-28 01:16:20", "md5": "6fb589bbf8a1f6e7e571a866e66ad6d8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R2-T2_S8_L003_R2_001.fastq.gz", "size": "2697518678", "date": "2019-06-28 01:15:27", "md5": "1815fb1086902ba40c90eb0502e8e251", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609671", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609671/SRR9609671", "size": "3078929534", "date": "2019-06-28 01:17:51", "md5": "ef01f76670687e1484332be3b30fd3cb", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609671.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/609/SRR9609671.sralite.1", "size": "2239981986", "date": "2020-06-21 05:58:34", "md5": "262e718fc0eba9e0181c7f16eca7fa3d", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]