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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 11, 2023 |
| Title |
Dynamic enhancer landscapes in human craniofacial development [mouse ChIP] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. To annotate the cell type specificity of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating across these data sets, we identify major cell populations of the developing face and annotate over 16,000 candidate enhancers by their cell type-specific epigenomic profile. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we show the value of these data for the prediction of in vivo cell type specificity. Taken together, our data provide a critical resource for genetic and developmental studies of human craniofacial development.
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| Overall design |
We combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution.
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| Contributor(s) |
Rajderkar S, Paraiso K, Amaral ML, Kosicki M, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio L, Visel A |
| Citation(s) |
38448444 |
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| Submission date |
Jun 26, 2023 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Laura E Cook |
| E-mail(s) |
lecook@lbl.gov
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| Organization name |
Lawrence Berkeley National Laboratory
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| Department |
Biosciences
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| Lab |
MFGL
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| Street address |
1 Cyclotron Road
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| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (20)
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| GSM7508817 |
mandibular process, e15.5, input |
| GSM7508818 |
maxillary process, e15.5, input |
| GSM7508819 |
nose, e15.5, H3K27 input |
| GSM7508820 |
mandibular process, e11.5, H3K27ac |
| GSM7508821 |
maxillary process, e11.5, H3K27ac |
| GSM7508822 |
medial nasal plate, e11.5, H3K27ac |
| GSM7508823 |
lateral nasal plate, e11.5, H3K27ac |
| GSM7508824 |
mandibular process, e11.5, input |
| GSM7508825 |
maxillary process, e11.5, input |
| GSM7508826 |
medial nasal plate, e11.5, input |
| GSM7508827 |
lateral nasal plate, e11.5, input |
| GSM7508828 |
mandibular process, e13.5, H3K27ac |
| GSM7508829 |
maxillary process, e13.5, H3K27ac |
| GSM7508830 |
nose, e13.5, H3K27ac |
| GSM7508831 |
mandibular process, e13.5, input |
| GSM7508832 |
maxillary process, e13.5, input |
| GSM7508833 |
nose, e13.5, input |
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| This SubSeries is part of SuperSeries: |
| GSE235858 |
Dynamic enhancer landscapes in human craniofacial development |
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| Relations |
| BioProject |
PRJNA987562 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235748_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of BROADPEAK, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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