EXPERIMENT_TITLE: GSM2745898: HelaS3-NS; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 3 ml of 16% formaldehyde solution was added to the 50  ml tube to obtain a  final  concentration of 1%. The content was quickly mixed by inverting the tube twice and left at RT for 10 min for cross-linking.  2.5  ml  of  2.5  M  glycine  was  then  added  to  the  tube to  stop  cross-linking.  The content was quickly mixed by inverting the tube twice and left at RT for 5 min, and then on ice for at least 15 min.  Subsequently, cells were collected by centrifugation (2000 rpm, 10 min), and the cell pellet was frozen on dry ice and then stored at -80°C. HiC was performed as in Belton et. al, 2012, http://www.sciencedirect.com/science/article/pii/S1046202312001168?via%3Dihub
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Mitotic chromosome morphogenesis occurs through condensin-mediated disassembly of the interphase conformation and formation of extended prophase loop arrays that then shorten by condensin-dependent helical winding Overall design: Chromosome organization investigation through Hi-C
SAMPLE_TITLE: HelaS3-NS
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HelaS3-CCL2.2"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "phase", "VALUE": "NS"}]
Pool_Member_@attributes_sample_title: HelaS3-NS
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HelaS3-NS
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CCHiC-HeLa-NS-R1_23-05-2011_s_5_2_fastq.gz", "size": "1709305221", "date": "2020-03-23 00:27:02", "md5": "50b1b69d18ddf69e272615ed575b3aae", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CCHiC-HeLa-NS-R1_23-05-2011_s_5_1_fastq.gz", "size": "1704183284", "date": "2020-03-23 00:29:54", "md5": "569ab07eab778fc06516cef6889b5709", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5939760.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/939/SRR5939760.sralite.1", "size": "1158832863", "date": "2020-06-21 01:24:07", "md5": "54f905da6895c5250fc9f45f4240489e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5939760", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5939760/SRR5939760", "size": "1925503083", "date": "2017-08-16 17:05:18", "md5": "171b5b2e22a39443e8ce1a65a3db1d1d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]