EXPERIMENT_TITLE: GSM3909732: R3: 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: R3: 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: R3: released 2.5 hours
RUN_SET_RUN_Pool_Member_@attributes_sample_title: R3: released 2.5 hours
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R3-T25-R3-T1_S15_L005_R1_001.fastq.gz", "size": "6152449107", "date": "2019-06-28 02:09:37", "md5": "0861e585fef4c8b14199bb77a97e7d52", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TB-HiC-Dpn-R3-T25-R3-T1_S15_L005_R2_001.fastq.gz", "size": "6344652624", "date": "2019-06-28 02:05:08", "md5": "b70ec8625cb5ca78c3433b846c3a9a53", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9609705.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/609/SRR9609705.sralite.1", "size": "4953693534", "date": "2020-06-20 00:15:22", "md5": "2267e25355858371d7c6ec5a8c8d1bca", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9609705", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9609705/SRR9609705", "size": "7386671342", "date": "2019-06-28 02:14:30", "md5": "846842d22468b0e25a181fe6c3cdc6a3", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]