EXPERIMENT_TITLE: GSM7114667: Gluta_HiC_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: HiC and Capture-C: Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with Arima enzyme cocktail. Capture-C: Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with DpnII. HiC and Capture-C: HiC was performed in iCell GlutaNeurons, and Capture-C was performed in iCell GlutaNeurons and GABANeurons. All experiments were performed in triplicate with independent cell grow-ups of approximately 15 million cells for biological replication. For HiC, we followed manufacturer recommendations from the Arima HiC kit- User Guide for Mammalian cell lines (A510008, V.Oct.2019) using the Arima HiC Library Prep using Swift Biosciences Accel-NGS 2S plus DNA library kit (A510008, V. Nov2018). iCell GlutaNeuron and GABANeuron Capture-C was performed following the HiC protocols, with the addition of the Agilent Technology SureSelect XT HS/SureSelect XT Low input target enrichment with pre-capture pooling protocol. 102 SureSelect DNA probes spanning a 2kb region (chr17:45892780-45893184 and chr17:45893527-45895196; hg38) were ordered from AgilentTechnologies. The region between the two probes could not be synthesized because of low sequence complexity. Capture-C: Capture-C was performed in NPCs, Day 14 BrainPhys differentiated neurons. All experiments were performed in triplicate with independent cell grow-ups of approximately 15 million cells for biological replication. NPC and Day 14 BrainPhys differentiated neuron Capture-C was performed following the NG Capture-C Protocol (v2.4).46 For this experiment, enrichment for MAPT promoter contacts was performed by double capture using two biotinylated oligonucleotides targeting chr17:45892836–45892923 and chr17:45895092–45895179 (both hg38)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Tau is encoded by MAPT and abnormal aggregates of tau are a hallmark of a group of neurodegenerative diseases called tauopathies. MAPT is lowly expressed in neural progenitor cells (NPCs), but it is more highly expressed in oligodendrocytes, astrocytes, and neurons that derive from NPCs. This expression switch at differentiation suggests that MAPT expression is controlled by transcription factors and cis-regulatory elements specific to these differentiated cell types, including neurons. Overall design: We performed HiC and three-dimensional chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq and ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in neurons differentiated from human iPSC cultures. From these methods, we nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, NPCs differentiated to neurons, and pure inhibitory or excitatory neuron cultures. We then functionally assessed nominated regions using luciferase assays and CRISPR dCas9-KRAB inhibition experiments to assess the effect of nominated regions on MAPT expression.
SAMPLE_TITLE: Gluta_HiC_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "iCell Gluta"}, {"TAG": "cell line", "VALUE": "iCell Gluta"}, {"TAG": "cell type", "VALUE": "Gluta Neurons"}]
Pool_Member_@attributes_sample_title: Gluta_HiC_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Gluta_HiC_rep1
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