EXPERIMENT_TITLE: GSM7173199: D70 HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed on 8-10 organoids from each time point according to the manufacturer's instruction of Arima Genomics. In brief, organoids were dissociated to single cell following an optimized protocol of papain system (Fadl, et al., 2020) and then crosslinked with 2% paraformaldehyde (PFA, FDNeuroTechnologies) for 10 min. Subsequently, the crosslinked samples were quenched by 125 mM glycine for 5 min and frozen until use at -80 ℃ until use for Hi-C experiments. Freshly dissected human retina tissue was crosslinked with 1% formaldehyde in PBS for 10 min, quenched with 125 mM glycine for 5 min and frozen until use for Hi-C experiments. Before processing for Hi-C, samples were crosslinked again in 2% formaldehyde for 10 minutes, then quenched with 125 mM glycine 5 min. For HCT116 cell line (ATCC, VA, USA), 7x106 cells were crosslinked with 2% formaldehyde for 10 min, quenched for 5 min with stop solution I, lysed, and processed for Hi-C using ARIMA-Hi-C kit. Hi-C was performed on isolated nuclei using Arima-Hi-C kit (Arima Genomics, CA, USA) and Hyper Prep DNA-seq library prep kit (KK8502; Kapa Biosciences, MA, USA), following the manufacturers' instructions. The libraries were sequenced on HiSeq 2500 platform (Illumina, CA, USA) at a read length of 101 to 126 base pairs and approximately 600 million read pairs per sample.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We have generated high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive and developmental stage-specific alterations in DNA topology and correlate these changes with transcription of cell type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift towards A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages of TADs (i.e., TAD cliques) tend to localize in the active chromatin regions with binding sites for eye-field transcription factors. These genes show a gain of chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits. Overall design: High resolution Hi-C at five time points in retinal organoid development (D60, D70, D90, D120, D200).
SAMPLE_TITLE: D70 HiC
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