EXPERIMENT_TITLE: GSM5134423: HiC_KO_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: RNA-seq: RNA extraction was performed using RNeasy mini-kit (Qiagen) followed by Turbo DNA-free kit (Ambion).  ChIP-seq: Cells were collected with or without formaline fixation. Chromatin was fragmented by MNase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies. DNA was purified using MinElute columns from Qiagen.  Hi-C: Cells were fixed with 2% of formaldehyde, chromatin was digested with DpnII, DNA ends were biotinylated and re-ligated in situ. DNA was purified by reverse-crosslinking, followed by phenol/chloroform extraction, ethanol precipitation and additional purification using AMPure XP magnetic beads. DNA was sheared by sonication, ligation junctions were enriched by Biotin pull-down. RNA-seq: Libraries were constructed using Truseq stranded total RNA kit (Illumina).  ChIP-seq: Libraries were prepared using the MicroPlex V2 library preparation kit (Diagenode).  Hi-C: Libraries were prepared with standard protocol using TruSeq adapters (Illumina).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Imbalance in the finely orchestrated system of chromatin-modifying enzymes is a hallmark of many pathologies such as cancers, since causing the affection of the epigenome and transcriptional reprogramming. Here, we demonstrate that a loss-of function mutation of the major histone lysine methyltransferases SETDB1 possessing oncogenic activity in lung cancer cells leads to broad changes in the overall architecture and mechanical properties of the nucleus through redistribution of heterochromatin genome-wide, which perturbs chromatin spatial compartmentalization. Together with the enforced activation of the epithelial expression program, cytoskeleton remodeling, reduced proliferation rate, and restricted cellular migration, this leads to the reversed oncogenic potential of lung adenocarcinoma cells. These results emphasize an essential role of chromatin architecture in the determination of oncogenic programs and illustrate a relationship between gene expression, epigenome, 3D genome, and nuclear mechanics. Overall design: This submission contains RNA-seq, H3K9me3 ChIP-seq, H3K27me3 ChIP-seq, H3K27ac ChIP-seq, H3K4me3 ChIP-seq, CTCF ChIP-seq, and Hi-C experiments on Control (CT) and SETDB1 loss-of-function mutation (KO) A549 cells.
SAMPLE_TITLE: HiC_KO_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "A549 immortalized cell line"}, {"TAG": "cell line", "VALUE": "A549"}, {"TAG": "genotype", "VALUE": "SETDB1 knockout (KO)"}, {"TAG": "disease", "VALUE": "lung adenocarcinoma"}]
Pool_Member_@attributes_sample_title: HiC_KO_rep2
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