EXPERIMENT_TITLE: GSM5617593: Induced pluripotent stem cell Iso-T - HiC_rep3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: RNA was extracted utilizing RNeasy Plus Mini Kit (Qiagen). In situ Hi-C - Hi-C libraries were generated from 2 million iPSCs and NPCs using the Arima Hi-C kit (Arima Genomics, San Diego) following to the manufacturer's instructions without any modifications. Briefly, the Arima Hi-C kit consists of 6 steps: (i) cells were crosslinked with 1% formaldehyde, (ii) DNA was digested using the Arima restriction enzyme cocktail within intact permeabilized nuclei, (iii) ends were filled and biotinylated, (iv) blunt ends were ligated, (v) ligated fragments were purified, sheared and a biotin pull down was performed using streptavidin, and (vi) adapters were ligated, barcoded and amplified using the Kappa Hyperprep Kit (Roche, KK8502).    ChIP-seq - Library preparation consists of 8 steps: (i) cells were crosslinked with 1% formaldehyde, (ii) chromatin was sheared (Covaris E220 Focused-ultrasonicator) after lysing cells, (iii) digested chromatin was incubated with 2ug of LMNB1 antibody (Abcam, ab8982), samples were also incubated without any antibody for input and Spike-in chromatin was incubated with Spike-in antibody (Active motif). (iv) same amount of Spike-in chromatin/antibody was added to each sample. (V) antibody-bound DNA/protein complexes and input samples were captured and washed using Protein G magnetic beads. (vi) cross-links were reversed and protein was digested using proteinase K. (vii) DNA was purified utilizing QIAquick PCR Purification Kit (Qiagen, 28104) (viii) libraries were prepared utilizing the Kappa Hyperprep Kit (Roche, KK8502).    ATAC-seq - Libraries were prepared as previously described (Buenrostro et al., 2015).    RNA-seq - 150 ng of RNA was used to prepare libraries using the Kapa mRNA hyperprep kit for standard RNA libraries (Roche, KK8540) on a TecanEvo 150s (Tecan).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We utilized human derived induced pluripotent stem cells (iPSCs) and iPSC derived neural progenitor cells (NPCs) from individuals with Down syndrome and sex matched controls to interrogate the cell type consequences of trisomy 21 (T21). We report the consequences of T21 on the spatial chromatin organization (Hi-C), lamina-associated domains (ChIP-seq), chromatin state (ATAC-seq), and transcriptome (RNA-seq)  in an isogenic pair (euploid: Iso-E and trisomic: Iso-T cells derived from the same individual), pair of male individuals with euploid (Ma-E) and trisomic (Ma-T), pair of female individuals with euploid (Fe-E) and trisomic (Fe-T). Our findings show that T21 induces chromosomal introversion, disrupts lamina-associated domains (LADs) and alters the genome-wide chromatin-accessibility of NPCs but not iPSCs. While the overall organization of A/B compartments and location of TAD-boundaries are conserved in NPCs harboring T21, we observe loss of chromatin-accessibility within the A-compartment that is associated with transcriptional downregulation, and increased long-range chromatin interactions in the B-compartment that is associated with transcriptional upregulation. We find that these architectural changes are similar to those observed in senescent cells, and our transcriptional analysis confirms that differentially expressed genes (DEGs) identified in NPCs harboring T21 are highly correlated with DEGs identified in oxidative stress induced senescent cells. Finally, we demonstrate that the senolytic drug combination of dasatinib and quercetin alleviates the genome-wide transcriptional disruption, as well as deficits in cellular migration and proliferation observed in NPCs harboring T21. Overall design: Decoding the impact trisomy 21 (T21) on the 3D-genome organization, lamina-associated domains, epigenome and transcriptome of human derived induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs).
SAMPLE_TITLE: Induced pluripotent stem cell Iso-T - HiC_rep3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Induced Pluripotent Stem Cells"}, {"TAG": "cell type", "VALUE": "Induced Pluripotent Stem Cells"}, {"TAG": "strain", "VALUE": "Down syndrome"}, {"TAG": "chip antibody", "VALUE": "none"}, {"TAG": "treatment", "VALUE": "untreated"}, {"TAG": "cell line", "VALUE": "AG05397"}]
Pool_Member_@attributes_sample_title: Induced pluripotent stem cell Iso-T - HiC_rep3
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Induced pluripotent stem cell Iso-T - HiC_rep3
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