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| Status |
Public on May 25, 2020 |
| Title |
Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing |
| Organisms |
Escherichia coli; Staphylococcus aureus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline. We demonstrated that PETRI-seq effectively barcoded single bacterial cells in a species-mixing experiment with E. coli (MG1655) and S. aureus (USA300). Within the S. aureus population, we found rare prophage induction in 0.04% of cells. We further demonstrated that PETRI-seq was able to distinguish between E. coli growth phases based on mRNA expression patterns by combining stationary E. coli with exponential E. coli in multiple experiments.
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| Overall design |
Eight libraries were prepared by PETRI-seq, including species-mixed libraries of E. coli and S. aureus and/or E. coli cells in distinct growth stages (stationary, exponential). PETRI-seq libraries are detailed in Supplementary Table 4. Ten bulk libraries were prepared, including nine E. coli libraries and one S. aureus library.
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| Contributor(s) |
Blattman SB, Jiang W, Oikonomou P, Tavazoie S |
| Citation(s) |
32451472 |
| |
| Submission date |
Nov 26, 2019 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Sydney B Blattman |
| E-mail(s) |
sb3292@columbia.edu
|
| Organization name |
Columbia University
|
| Lab |
Tavazoie Lab
|
| Street address |
1150 St. Nicholas Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platforms (3) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
| GPL24034 |
Illumina NextSeq 500 (Staphylococcus aureus) |
| GPL27809 |
Illumina NextSeq 500 (Escherichia coli; Staphylococcus aureus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA591783 |
| SRA |
SRP233278 |
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