|
| Status |
Public on Nov 11, 2021 |
| Title |
A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity |
| Organisms |
Escherichia coli; Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
We developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell-types simultaneously. As a proof of concept, we assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay. Our results show that housekeeping promoters and CpG island promoters have lower activity in K562 cells relative to HEK293, which likely reflects developmental differences between the cell lines. Within K562 cells, scMPRA identified a subset of developmental promoters that are upregulated in the CD34+/CD38- sub-state, confirming this state as more “stem-like.” Finally, we deconvolved the intrinsic and extrinsic components of cell-to-cell variability and found that developmental promoters have a higher proportion of extrinsic noise compared to housekeeping promoters. We anticipate scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.
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| Overall design |
single-cell massively parallel reporter assay of a core promoter library with 676 members and each sequence is barcoded 3 times with a 16 bp DNA barcode. A second 25 bp random barcodes was added during cloning. The library was sequencd using bulk RNA-seq and single-cell RNA-seq in K562 and HEK293 cells. Each experiment contains 2 replicates.
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| |
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| Contributor(s) |
Zhao S, Hong CK, Myers CA, Granas DM, White MA, Corbo JC, Cohen BA |
| Citation(s) |
36635387 |
| |
| Submission date |
Nov 11, 2021 |
| Last update date |
Jun 06, 2025 |
| Contact name |
SIQI ZHAO |
| E-mail(s) |
szhao@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Cohen
|
| Street address |
Campus Box 8232 4515 McKinley Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL16085 |
Illumina MiSeq (Escherichia coli) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (19)
|
| GSM5687477 |
HEK293 bulk barcodes rep1 [MPPRA] |
| GSM5687478 |
HEK293 bulk barcodes rep2 [MPPRA] |
| GSM5687479 |
Mixed cell single-cell transcriptome rep1 [scRNA-seq] |
| GSM5687480 |
Mixed cell single-cell transcriptome rep2 [scRNA-seq] |
| GSM5687481 |
K562 single-cell transcriptome rep1 [scRNA-seq] |
| GSM5687482 |
K562 single-cell transcriptome rep2 [scRNA-seq] |
| GSM5687483 |
Mixed cell barcodes rep1 [scMPPRA] |
| GSM5687484 |
Mixed cell barcodes rep2 [scMPPRA] |
| GSM5687485 |
K562 cell barcodes rep1 [scMPPRA] |
| GSM5687486 |
K562 cell barcodes rep2 [scMPPRA] |
| GSM6614199 |
retina single-cell transcriptome rep1 [scRNA-seq] |
| GSM6614200 |
retina single-cell transcriptome rep2 [scRNA-seq] |
| GSM6614201 |
retina barcodes rep1 [scMPPRA] |
| GSM6614202 |
retina barcodes rep2 [scMPPRA] |
| GSM6614203 |
retina u6 barcodes rep1 [scMPPRA] |
| GSM6614204 |
retina u6 barcodes rep2 [scMPPRA] |
|
| Relations |
| BioProject |
PRJNA779733 |
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