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Series GSE228120 Query DataSets for GSE228120
Status Public on Apr 12, 2023
Title MAPT expression is mediated by long-range interactions with cis-regulatory elements [scMultiomics]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Contributor(s) Rogers BB, Anderson AG, Cochran JN
Citation(s) 37090552
Submission date Mar 23, 2023
Last update date Nov 21, 2023
Contact name J. Nicholas Cochran
Phone 2563275220
Organization name HudsonAlpha Institute for Biotechnology
Lab Cochran Lab
Street address 601 Genome Way
City Huntsville
State/province AL
ZIP/Postal code 35806
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (6)
GSM7114700 day0, scRNAseq
GSM7114701 day7, scRNAseq
GSM7114702 day14, scRNAseq
This SubSeries is part of SuperSeries:
GSE228121 MAPT expression is mediatedd by long-range interactions with cis-regulatory elements.
BioProject PRJNA948138

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE228120_atacfragments.tsv.gz 8.3 Gb (ftp)(http) TSV
GSE228120_atacfragments.tsv.gz.tbi.gz 2.2 Mb (ftp)(http) TBI
GSE228120_barcodes.tsv.gz 38.9 Kb (ftp)(http) TSV
GSE228120_features.tsv.gz 5.0 Mb (ftp)(http) TSV
GSE228120_matrix.mtx.gz 690.2 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data are available on Series record

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