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Series GSE217679 Query DataSets for GSE217679
Status Public on Dec 12, 2022
Title Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA_devCRE_mEBs]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. Our dual RNA strategy extends the range of expression measurement into a regime fundamentally inaccessible with traditional multiplex reporter systems, yielding an accurate readout of mRNA levels spanning four orders of magnitude and a precision approaching the limit set by Poisson (shot) noise. As a proof-of-concept experiment, we profile over two hundred putative developmental cis-regulatory elements (CREs) for cell-type-specific activity in a multicellular in vitro model of early mammalian development, identifying dozens of active elements, ten of which function in an autonomous, cell-type-specific manner. These include constituents of the canonical Sox2 control region, exclusively active in pluripotent cells, multiple parietal endoderm-specific enhancers, including at the Foxa2 and Gata4 loci, and a compact pleiotropic enhancer at the Lamc1 locus. Looking forward, we envision that scQers will be broadly useful in developmental systems to quantitatively profile the activity of native, perturbed, or synthetic enhancers at scale, with high sensitivity and at single cell resolution.
 
Overall design Bulk MPRA time series on mouse embryoid body induction from cells harboring high MOI genome-integrated dual RNA reporters (devCRE series), three biological replicates.

Experient type (submitter-provided): massively parallel reporter assay (bulk)
 
Contributor(s) Lalanne J, Regalado SG, Domcke S, Li T, Martin B, Calderon D, Suiter CC, Trapnell C, Shendure J
Citation(s) 38724692
Submission date Nov 10, 2022
Last update date Jun 28, 2024
Contact name Jean-Benoit Lalanne
E-mail(s) [email protected]
Organization name University of Washington
Department Genome Sciences
Lab Jay Shendure
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (80)
GSM6724837 bulk_MPRA_mEB_series_mBC_repA_d00_DNA
GSM6724838 bulk_MPRA_mEB_series_mBC_repB_d00_DNA
GSM6724839 bulk_MPRA_mEB_series_mBC_repA_d04_DNA
This SubSeries is part of SuperSeries:
GSE217690 Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
Relations
BioProject PRJNA900079

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

Supplementary file Size Download File type/resource
GSE217679_bulk_MPRA_counts_mEB_series.txt.gz 15.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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