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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 27, 2022 |
| Title |
Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler |
| Organisms |
Escherichia coli; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
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| Summary |
How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, we combined single-cell RNA-seq and single-cell ATAC-seq with cell-type-specific measurements of enhancer activity, DNA methylation and three-dimensional genome architecture to systematically map the regulatory landscape of neural differentiation in the mouse neocortex in vivo. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex.
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| Overall design |
scRNA-seq and scATAC-seq of the somsatosensory area of the E14.5 mouse cortex. Additionally, massively parallel reporter assay (MPRA) and MethylHiC from isolated cell populations, namely neuronal stem cells (NSC), intermediate progenitors (IPC), projection neurons (PN), obtained from the somatosensory area of the E14.5 mouse cortex. Functional validation of Neurog2 using Hi-C, RNA-seq and NOME-seq in GFP and Neurog2 in vivo overexpression via in utero electroporation.
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| Contributor(s) |
Noack F, Vangelisti S, Raffl G, Carido M, Diwakar J, Chong F, Bonev B |
| Citation(s) |
35132236 |
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| Submission date |
Aug 04, 2020 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Boyan Bonev |
| E-mail(s) |
boyan.bonev@helmholtz-munich.de
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| Organization name |
Helmholtz Zentrum München
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| Lab |
Bonev Lab
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| Street address |
Ingolstädter Landstr. 1
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| City |
Neuherberg |
| State/province |
Deutschland |
| ZIP/Postal code |
85764 |
| Country |
Germany |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL25368 |
Illumina NovaSeq 6000 (Escherichia coli) |
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| Samples (36)
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| GSM4710393 |
scRNA-seq E14.5 somatosensory cortex rep1 |
| GSM4710394 |
scRNA-seq E14.5 somatosensory cortex rep2 |
| GSM4710395 |
scATAC-seq E14.5 somatosensory cortex rep1 |
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| Relations |
| BioProject |
PRJNA655209 |
| SRA |
SRP275808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE155677_RAW.tar |
44.0 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BW, FA, MTX, PICKLE, TAR, TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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