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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 23, 2020 |
| Title |
Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
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| Summary |
In situ assays of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we use scCC to map the binding of BRD4 and three additional TFs in cultured cells. We then apply this technique to discover bromodomain-dependent cell state dynamics in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ.
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| Overall design |
1 bulk DNA calling card library, 8 bulk RNA calling card libraries, 9 single cell RNA-seq libraries, 9 single cell calling card libraries
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| Contributor(s) |
Moudgil A, Mitra RD |
| Citation(s) |
32710817, 38323623 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| F30 HG009986 |
Deciphering Cellular Heterogeneity with Single Cell Calling Cards |
WASHINGTON UNIVERSITY |
Arnav Moudgil |
| R21 HG009750 |
SINGLE-CELL ANALYSIS OF PIONEER BINDING AND FUNCTION DURING LINEAGE REPROGRAMMING |
WASHINGTON UNIVERSITY |
Robi D Mitra |
| R21 HG009750 |
SINGLE-CELL ANALYSIS OF PIONEER BINDING AND FUNCTION DURING LINEAGE REPROGRAMMING |
WASHINGTON UNIVERSITY |
Samantha Annette Morris |
| R01 GM126112 |
Dissecting mechanisms of pioneer transcription factor-mediated lineage reprogramming |
WASHINGTON UNIVERSITY |
Samantha Annette Morris |
| U01 MH109133 |
AN INDUCIBLE MOLECULAR MEMORY SYSTEM TO RECORD TRANSIENT STATES OF CNS CELLS |
WASHINGTON UNIVERSITY |
Robi D Mitra |
| RF1 MH117070 |
PARALLEL ANALYSIS OF TRANSCRIPTION AND PROTEIN-DNAINTERACTIONS IN SINGLE CNS CELLS |
WASHINGTON UNIVERSITY |
JOSEPH D DOUGHERTY |
| RF1 MH117070 |
PARALLEL ANALYSIS OF TRANSCRIPTION AND PROTEIN-DNAINTERACTIONS IN SINGLE CNS CELLS |
WASHINGTON UNIVERSITY |
Robi D Mitra |
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| Submission date |
Apr 10, 2020 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Robi D Mitra |
| E-mail(s) |
rmitra@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Street address |
4515 McKinley Ave
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| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63143 |
| Country |
USA |
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| Platforms (8)
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| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
| GPL22245 |
Illumina HiSeq 2500 (Homo sapiens; Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (27)
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| Relations |
| BioProject |
PRJNA624288 |
| SRA |
SRP255958 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148448_RAW.tar |
37.6 Gb |
(http)(custom) |
TAR (of BAM, CSV, LOOM, TSV, TXT) |
| GSE148448_README.txt |
1.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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