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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 07, 2023 |
| Title |
DNA methylation in the mouse cochlea promotes maturation of supporting cells and contributes to the failure of hair cell regeneration |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose - To profile epigenetic changes in cochlear progenitor cells, hair cells, and supporting cells across postnatal development. Methods- Cochlear cell types were obtained from fluorescently labeled transgenic mice. E13.5 cochlear prosensory progenitor cells (E13.5_PG, p27Kip1-GFP+), P1 hair cells (P1_HC, Atoh1-GFP+), P1 supporting cells (P1_SC, Lfng-GFP+), and P6, P8, P21 supporting cells (P6_SC, P8_SC, P21_SC, Lfng-creER, NuTRAP lineage-traced) were FACS purified for epigenetic profiling using WGBS (DNA methylation), CUT&Tag (H3K4me1, H3K4me3, H3K27me3, CUTAC H3K4me2). DNA demethylation of hair cell-specific promoters was interrogated by comparing % mCpG profiles of transdifferentiating supporting cells (P1_SC_tdt_gfp, Lfng-creER/TdTomato+, Atoh1-GFP+) against non-transdifferentiating supporting cells (P1_SC_tdt, P6_SC_tdt, Lfng-creER/TdTomato+) purified via FACS. P1 and P8 wildtype cochleas were enzymatically dissociated and used directly for scMultiome simultaneous profiling of RNA and ATAC at the single cell level (P1_scMultiome, P8_scMultiome, 10x Genomics). For scMultiome of P70 wildtype (P70_wt_scMultiome, Lfng-CreERT2, NuTRAP) and P70 deafened (P70_deaf_scMultiome, Lfng-CreERT2, NuTRAP, Pou4f3DTR) supporting cells, mice received 100 mg/kg tamoxifen (Sigma-Aldrich T5648) at P21, 0.01 mg/kg Diptheria toxin (Sigma-Aldrich D0564) at P28, and allowed to mature to P70, at which point cochlear tissues were harvested, FACS purified for NuTRAP+ supporting cells, and inputted into a scMultiome reaction. Results- WGBS highlighted differentially methylated regions (DMR) across E13.5_PG, P1_HC, P1_SC, P6_SC, and P21_SC. Pre-established DMRs become hypermethylated in supporting cells between P1 and P21. This corresponds with increasing heterochromatin characteristics, such as loss of accessibility (CUTAC), loss of H3K4me1, and switch between H3K27me3-mediated repression to DNA methylation-mediated silencing. WGBS of P1_SC_tdt_gfp compared to P1_SC_tdt and P6_SC_tdt showed DNA demethylation of hair cell-specific DMRs, suggesting that DNA demethylation is required for transdifferentiation of supporting cells into hair cells. P1_scMultiome, P8_scMultiome, P70_wt_scMultiome, and P70_deaf_scMultiome revealed changes in chromatin accessibility associated with age, as well as from long-term deafening at the single cell level. scMultiome datasets also highlight cell type-specific enhancers active during different stages of postnatal development.
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| Overall design |
Examination of epigenetic modifications of FACS purified mouse cochlear cells at P1, P6, P8, and P21. scMultiome ATAC + Gene Expression (10x genomics) experiments on P1 and P8 wildtype, as well as P70 wildtype and long-deafened cochlear sensory epithelia.
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/37549271/
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| Contributor(s) |
Groves AK, Segil N, Nguyen JD, Llamas J |
| Citation(s) |
37549271 |
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| Submission date |
Feb 05, 2023 |
| Last update date |
Sep 05, 2023 |
| Contact name |
John Duc Nguyen |
| E-mail(s) |
johndngu@usc.edu
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| Phone |
7143327231
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| Organization name |
USC
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| Department |
Stem Cell
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| Lab |
Segil Lab
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| Street address |
3711 Baldwin Street, Unit 602
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90031 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (52)
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| Relations |
| BioProject |
PRJNA931748 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE224563_DMR_de_novo_HC-specific.bed.gz |
58.3 Kb |
(ftp)(http) |
BED |
| GSE224563_DMR_de_novo_SC-specific.bed.gz |
27.1 Kb |
(ftp)(http) |
BED |
| GSE224563_DMR_de_novo_common.bed.gz |
82.8 Kb |
(ftp)(http) |
BED |
| GSE224563_DMR_pre-established.bed.gz |
25.3 Kb |
(ftp)(http) |
BED |
| GSE224563_P1_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSE224563_P1_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz |
4.0 Mb |
(ftp)(http) |
TSV |
| GSE224563_P1_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.mtx.gz |
302.0 Mb |
(ftp)(http) |
MTX |
| GSE224563_P1_wildtype_10x_scRNA_scATAC.h5seurat |
1.7 Gb |
(ftp)(http) |
H5SEURAT |
| GSE224563_P1_wildtype_10x_scRNA_scATAC_seurat.rds.gz |
1.0 Gb |
(ftp)(http) |
RDS |
| GSE224563_P70_cochlea_deafened_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
| GSE224563_P70_cochlea_deafened_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz |
2.7 Mb |
(ftp)(http) |
TSV |
| GSE224563_P70_cochlea_deafened_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.tsv.gz |
51.2 Mb |
(ftp)(http) |
TSV |
| GSE224563_P70_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz |
869.3 Kb |
(ftp)(http) |
TSV |
| GSE224563_P70_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
| GSE224563_P70_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.tsv.gz |
30.5 Mb |
(ftp)(http) |
TSV |
| GSE224563_P70_integrate_wildtype_deaf_10x_scRNA_scATAC.h5seurat |
954.8 Mb |
(ftp)(http) |
H5SEURAT |
| GSE224563_P70_integrate_wildtype_deaf_10x_scRNA_scATAC_seurat.rds.gz |
214.2 Mb |
(ftp)(http) |
RDS |
| GSE224563_P8_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSE224563_P8_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSE224563_P8_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.mtx.gz |
295.8 Mb |
(ftp)(http) |
MTX |
| GSE224563_P8_wildtype_10x_scRNA_scATAC.h5seurat |
1.2 Gb |
(ftp)(http) |
H5SEURAT |
| GSE224563_P8_wildtype_10x_scRNA_scATAC_seurat.rds.gz |
572.6 Mb |
(ftp)(http) |
RDS |
| GSE224563_RAW.tar |
9.5 Gb |
(http)(custom) |
TAR (of BW, COV, H5, TSV) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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