EXPERIMENT_TITLE: GSM3756152: Hi-C MCF7 mid Replicate 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were cross-linked with formaldehyde, lysed and the intact nuclei was permeabilized. DNA was then cut with NcolI restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads. Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing using the NEBNext DNA Master Mixes kit and the ligation of universal adapter was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Around 35% of Estrogen Receptor (ER) positive patients develop resistance and relapse, highlighting the need to further understand the mechanisms underpinning endocrine resistance in breast cancer. Here, we study 3-dimensional (3D) epigenome remodelling in endocrine resistant breast cancer cells. We show that chromatin interactions both within and between topologically associating domains (TADs) frequently change in resistant breast cancer cells and that alterations in active (A-type) and inactive (B-type) chromosomal compartments are associated with decreased ER binding and atypical interactions and gene expression. Finally, we identify differentially interacting ER-bound regions that preferentially connect active enhancers and promoters associated with altered expression of ER-regulated genes. Importantly, interactions specifically associated with endocrine resistance, often occur coincidently with hypermethylation of ER binding. Our results demonstrate that 3D epigenome remodelling is a key mechanism of endocrine resistance that consists of differential chromatin interactions and aberrant DNA methylation at ER-regulated enhancer regions. Overall design: Hi-C was conducted in endocrine-sensitive breast cancer cells (MCF7) at three time-points during long-term culture: time zero (T0), time point mid and late time point (> 6 months)
SAMPLE_TITLE: Hi-C MCF7 mid Replicate 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MCF7"}, {"TAG": "cell line", "VALUE": "MCF7"}, {"TAG": "tissue", "VALUE": "breast cancer"}, {"TAG": "resistant phynotype", "VALUE": "responsive"}]
Pool_Member_@attributes_sample_title: Hi-C MCF7 mid Replicate 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C MCF7 mid Replicate 2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9030112", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9030112/SRR9030112", "size": "6204048869", "date": "2019-05-08 14:42:32", "md5": "3619b5788edbca364265efde1fe6776a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9030112.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/030/SRR9030112.sralite.1", "size": "3848369265", "date": "2020-06-19 19:36:33", "md5": "735d678f1c0ced4cde30e7e6e3fc993a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "20190418_Hi-C_MCF7Caldon_p16_a2_R2.fastq.gz", "size": "4663256949", "date": "2020-01-17 19:21:25", "md5": "2e45aca45ccd533b65ff563c095c1ae7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "20190418_Hi-C_MCF7Caldon_p16_a2_R1.fastq.gz", "size": "4461887818", "date": "2020-01-17 19:08:30", "md5": "8a6f485c886ad86bd776798cd253b2c1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]