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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 17, 2023 |
| Title |
Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [scQer_mEB, v2)] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, these scalable single-cell quantitative expression reporters (scQers) provide high-contrast readouts, analogous to classic in situ assays, but entirely from sequencing. Screening >200 putative enhancers in a multicellular in vitro model of early mammalian development, we identified thirteen (eight previously uncharacterized) autonomous and cell-type-specific elements, such as constituents of the Sox2 control region exclusively active in pluripotent cells, endoderm-specific enhancers, including near Foxa2 and Gata4, and a compact pleiotropic enhancer at the Lamc1 locus. We further demonstrate that synthetic enhancer pairs generate cognate two-cell-type activity profiles and assess gain/loss-of-function multicellular expression phenotypes from enhancer variants with perturbed transcription factor binding sites. scQers can be applied in developmental systems to quantitatively characterise native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution.
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| Overall design |
Single-cell reporter on day 24 mouse embryoid bodies with high MOI genome-integrated dual RNA reporters with literature-selected CREs, mutated CREs (allelic series of transcription factor binding sites), and paired CREs. Three biological replicates. Gene expression and custom oBC, mBC libraries.
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| Contributor(s) |
Lalanne J, Regalado SG, Domcke S, Li T, Li X, Martin B, Calderon D, Suiter CC, Trapnell C, Shendure J |
| Citation(s) |
38724692 |
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| Submission date |
Oct 12, 2023 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Jean-Benoit Lalanne |
| E-mail(s) |
[email protected]
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| Organization name |
University of Washington
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| Department |
Genome Sciences
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| Lab |
Jay Shendure
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL30172 |
NextSeq 2000 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE217690 |
Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters |
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| Relations |
| BioProject |
PRJNA1027347 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE245189_GEx_obj_sc_rep_mEB_series_v2.RDS.gz |
2.7 Gb |
(ftp)(http) |
RDS |
| GSE245189_assigned_oBC_CRE_mBC_joined_counts_sc_rep_mEB_series_v2.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE245189_mBC_poly_dT_counts_sc_rep_mEB_v2.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE245189_oBC_counts_sc_rep_mEB_v2.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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