EXPERIMENT_TITLE: GSM7598112: Rejuvenation Replicate2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were fixed with formaldehyde followed by quenching using 1M Glycine. Fixed cells were then processed for cell lyses using cell lyses buffer followed by restriction digetion with HindIII ovenight. Digested genome was end repair followed by DNA ligation, purification of HiC DNA using ethanol precepitation. HiC libraires were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional and genome-wide chromatin organization changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq and Hi-C experiments. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state, showed a reorganization of the inter-chromosomal contacts and lamina-associated domains. Interestingly, the observed chromatin reorganization correlated with the transcriptional changes. Immunofluorescence experiments in the rejuvenated state confirmed increased contractility and reduced chromosome copy number variations, similar to younger fibroblasts. In addition, the rejuvenated contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation. Overall design: To investigate chromatin interaction frequencies differences among the aged fibroblast we establisehed young 10 year age GM09503 and 75 year aged GM08401 human dermal fibroblast. On ther hand we allow to grow the 75 year aged fibroblast on fixed micropatterns to achieve partial reprogramming state up until 8 day. At 8 day spheroid stage cells were then re-differerntiated called rejuvenation using collagen gel with 1 mg/ml for 48 hours. Cells after 48 hours were isolated as single cells using collaginase enzyme treatment followed by culture them on normal cell culture dish. We then prepare three cell types for HiC DNA preparation using standarad in-nucleus HiC procedure.
SAMPLE_TITLE: Rejuvenation Replicate2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "GM08401_RF"}, {"TAG": "cell line", "VALUE": "GM08401_RF"}, {"TAG": "cell type", "VALUE": "Dermal Fibroblast"}, {"TAG": "genotype", "VALUE": "Wild type"}, {"TAG": "treatment", "VALUE": "Reprogrammed and re-differentiaed"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Rejuvenation Replicate2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Rejuvenation Replicate2
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