EXPERIMENT_TITLE: GSM5552624: Hi-C Rad21-OE; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The in situ Hi-C libraries was performed as previously described (Rao et al., 2014). Briefly, cells were grown to about 70%-80 % confluence, washed with PBS, fixed in 1% formaldehyde were suspended in Hi-C lysis buffer, to which 100 U MobI restriction enzyme (NEB, R0147) was added for overnight chromatin digestion. Free ends were labeled with biotin and then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500 bp and then biotinylated ligation junctions were recovered with streptavidin beads. Hi-C libraries were amplified using PCR and constructed according to the NEBnext library preparation protocol (NEB, E7335) and sequenced on the Illumina HiSeq X Ten platform.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: In eukaryotes, the nuclear chromatin in the interphase is a hierarchical organization. Previous studies have suggested that cohesin-DNA interactions play important architectural functions for chromatin structure in the interphase. In this study, we applied super-resolution imaging, single-molecule imaging to measure the distribution of cohesin subunits. Hi-C and RNA-seq were used to reveal the 3D genome structures alterations and the relationship with breast cancer upon Rad21 up-regulation. Hi-C experiment showed that the contact frequency of short distance was increased while that of long distance was decreased in the absence of Rad21 up-regulation. Chromatin interactions between A and B compartments increased and compartmentalization strength was reduced significantly upon Rad21 up-regulation. Correspondingly, accumulated contacts were shown at TAD corners and inter-TAD interactions increased. These observations support cohesin loop extrusion model and lead us to propose the unique role of Rad21-loader interaction in cohesin loading and further cohesin extrusion. Moreover, we combined transcriptome changes and chromatin structure alterations upon Rad21 up-regulation and revealed the correlation between Rad21 and breast cancer by affecting chromatin architecture. Overall design: Analysis of 3D genome architecture and gene expression data in control and Rad21 overexpression HeLa cell lines.
SAMPLE_TITLE: Hi-C Rad21-OE
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HeLa cells"}, {"TAG": "cell line", "VALUE": "HeLa-S3"}, {"TAG": "genotype/variation", "VALUE": "Rad21-OE"}]
Pool_Member_@attributes_sample_title: Hi-C Rad21-OE
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C Rad21-OE
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15687221.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR015/15687/SRR15687221/SRR15687221.lite.1", "size": "15623878643", "date": "2022-09-27 20:24:27", "md5": "4042f8692f83398b974255c47ab2bf1a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15687221", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15687221/SRR15687221", "size": "23559526835", "date": "2021-09-01 23:58:09", "md5": "5d194a0f15c2dbbfa94f32e9eacdee2d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "OE_R2_clean.fq.gz", "size": "16286086444", "date": "2021-09-01 23:46:22", "md5": "025b204a8cb80d21c60d3b24078e4bcb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "OE_R1_clean.fq.gz", "size": "15049756590", "date": "2021-09-01 23:42:44", "md5": "3f51729e822c79c874df6727add4451d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]