EXPERIMENT_TITLE: GSM3392704: HiC in CAPH2 KD, replicate 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ Hi-C was performed as previously described (Rao et al., 2014, Cell) Sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc). in situ HiC
STUDY_DESCRIPTOR_STUDY_ABSTRACT: ARID1A, a subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, influences gene accessibility. However, the role of ARID1A in spatial genomic organization and chromosomal interaction remains elusive.  We showed that the SWI/SNF complex interacts with condensin II and they show significant overlapping distributions in enhancers.  ARID1A inactivation drives redistribution of condensin II preferentially at enhancers without affecting the interaction between the SWI/SNF and condensing II complexes.   ARID1A and condensin II contribute to transcriptionally inactive B compartments, while ARID1A weakens the borders of topologically associated domains.  ARID1A inactivation decreases the frequency of genomic interactions over distance, but increases the intermixing of interphase small chromosomes, which was validated by three dimensional chromosome painting.  These results demonstrated ARID1A spatially partitions genome and chromosomes. Overall design: RNA-seq, CHIP-seq and HiC in ARID1A/CAPH2 WT, ARID1A KO and CAPH2 KD cell lines
SAMPLE_TITLE: HiC in CAPH2 KD, replicate 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "RMG1_shCAPH2"}, {"TAG": "cell line", "VALUE": "RMG1"}, {"TAG": "arid1a", "VALUE": "WT"}, {"TAG": "caph2", "VALUE": "KD"}]
Pool_Member_@attributes_sample_title: HiC in CAPH2 KD, replicate 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC in CAPH2 KD, replicate 2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HIC.CAPH2.KD.2_R1.fastq.gz", "size": "8274304474", "date": "2020-02-13 09:51:23", "md5": "480cfc30a0f82198dfb3a4b4e5518c2c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7853975", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7853975/SRR7853975", "size": "11096255120", "date": "2018-09-17 16:20:27", "md5": "3e1e497c431448df58294bf6ec2c82e4", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7853975.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR007/853/SRR7853975.sralite.1", "size": "7567313748", "date": "2020-06-14 13:06:32", "md5": "185cd05dd9ef3248047389b02a3721bd", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HIC.CAPH2.KD.2_R2.fastq.gz", "size": "8601704660", "date": "2020-02-13 10:27:13", "md5": "97c6408f74acbeecf19c739bd2365965", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]