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| Status |
Public on Feb 09, 2023 |
| Title |
Improved bacterial single-cell RNA-seq through automated MATQ-seq [bulk RNA-seq] |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol (MATQ-seq), providing enhancements that achieve a higher cell throughput while also including integration of automation. We selected a more efficient reverse transcriptase which led to a lower drop-out rate and higher workflow robustness, and we also successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. Applying this improved protocol on a large set of single Salmonella cells sampled over growth revealed improved gene coverage and a higher gene detection limit, allowing us to reveal the expression of small regulatory RNAs such as GcvB or CsrB at a single-cell level. In addition, we were able to confirm previously described phenotypic heterogeneity in Salmonella in regards to expression of pathogenicity-associated genes.
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| Overall design |
Bulk RNA-seq matching four growth phases used in parallel with single cell sequencing from Salmonella enterica serovar Typhimurium.
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| Contributor(s) |
Homberger C, Hayward RJ, Barquist L, Vogel J |
| Citation(s) |
36880749 |
| |
| Submission date |
Nov 23, 2022 |
| Last update date |
May 12, 2023 |
| Contact name |
Regan Hayward |
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2 / D15
|
| City |
Wurzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL30637 |
NextSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE218633 |
Improved bacterial single-cell RNA-seq through automated MATQ-seq |
|
| Relations |
| BioProject |
PRJNA904726 |
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