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| Status |
Public on Dec 10, 2024 |
| Title |
An Improved Bacterial Single-cell RNA-seq Reveals Biofilm Heterogeneity [scRNA-seq] |
| Organisms |
Staphylococcus aureus; Escherichia coli str. K-12 substr. MG1655; Caulobacter vibrioides NA1000 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In contrast to mammalian cells, bacterial cells lack mRNA polyadenylated tails, presenting a hurdle in isolating mRNA amidst the prevalent rRNA during single-cell RNA-seq. This study introduces a novel method, Ribosomal RNA-derived cDNA Depletion (RiboD), seamlessly integrated into the PETRI-seq technique, yielding RiboD-PETRI. This innovative approach offers a cost-effective, equipment-free, and high-throughput solution for bacterial single-cell RNA sequencing (scRNA-seq). By efficiently eliminating rRNA reads and substantially enhancing mRNA detection rates (up to 92%), our method enables precise exploration of bacterial population heterogeneity. Applying RiboD-PETRI to investigate biofilm heterogeneity, distinctive subpopulations marked by unique genes within biofilms were successfully identified. Notably, PdeI, a marker for the cell-surface attachment subpopulation, was observed to elevate cyclic diguanylate (c-di-GMP) levels, promoting persister cell formation. Thus, we address a persistent challenge in bacterial single-cell RNA-seq regarding rRNA abundance, exemplifying the utility of this method in exploring biofilm heterogeneity. Our method effectively tackles a long-standing issue in bacterial scRNA-seq: the overwhelming abundance of rRNA. This advancement significantly enhances our ability to investigate the intricate heterogeneity within biofilms at unprecedented resolution.
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| Overall design |
We performed a new single-cell library construction method for three species of bacteria: Escherichia coli MG1655, Caulobacter crescentus strain NA1000, Staphylococcus aureus 25923 and verified the effect of different treatments during library construction on library data.
And then we analyzed the single-cell sequencing datas by Seurat(version 4.3.0; http://satijalab.org/seurat/).
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| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 28, 2024 |
| Last update date |
Dec 11, 2024 |
| Contact name |
Xiaodan Yan |
| E-mail(s) |
[email protected]
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| Phone |
13283874287
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| Organization name |
Wuhan University
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| Department |
Medical Research Institute
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| Street address |
Donghu Road, No. 115, Wuchang District,
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| City |
Wuhan |
| State/province |
Hubei Province |
| ZIP/Postal code |
430071 |
| Country |
China |
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| Platforms (3) |
| GPL26592 |
Illumina NovaSeq 6000 (Escherichia coli str. K-12 substr. MG1655) |
| GPL27158 |
Illumina NovaSeq 6000 (Staphylococcus aureus) |
| GPL34253 |
Illumina NovaSeq 6000 (Caulobacter vibrioides NA1000) |
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| Samples (19)
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| GSM8117637 |
EC-24h-static-ΔΔ, replicate 1, scRNA-seq, High sequencing depth results (1214-7) |
| GSM8117638 |
EC-24h-static-ΔΔ, replicate 2, scRNA-seq, High sequencing depth results (1214-8) |
| GSM8117639 |
EC-3h-ΔΔ, replicate 1, scRNA-seq (0427-3) |
| GSM8117640 |
EC-3h-ΔΔ, replicate 2, scRNA-seq (0427-4) |
| GSM8117641 |
EC-3h, replicate 1, scRNA-seq (0615-1) |
| GSM8117642 |
EC-3h, replicate 2, scRNA-seq (0615-2) |
| GSM8117643 |
SA-3h, replicate 1, scRNA-seq (0119-E) |
| GSM8117644 |
SA-3h, replicate 2, scRNA-seq (0119-F) |
| GSM8117645 |
SA-3h-ΔΔ-replicate 1, scRNA-seq (0612-1) |
| GSM8117646 |
SA-3h-ΔΔ-replicate 2, scRNA-seq (0612-2) |
| GSM8117647 |
CC--3h, replicate 1, scRNA-seq (0225-1) |
| GSM8117648 |
CC--3h, replicate 2, scRNA-seq (0225-2) |
| GSM8117649 |
CC--3h, replicate 3, scRNA-seq (0225-3) |
| GSM8117650 |
CC-3h-ΔΔ-replicate 1, scRNA-seq (0225-4) |
| GSM8117651 |
CC-3h-ΔΔ-replicate 2, scRNA-seq (0225-5) |
| GSM8117652 |
CC-3h-ΔΔ-replicate 3, scRNA-seq (0225-6) |
| GSM8117653 |
SA-9h, scRNA-seq, High sequencing depth results (0609-7) |
| GSM8117654 |
CC-3h, scRNA-seq, High sequencing depth results (0129-3) |
| GSM8117655 |
EC-3h-ΔΔ, scRNA-seq, High sequencing depth results (0427-3_HSD) |
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| This SubSeries is part of SuperSeries: |
| GSE260458 |
An Improved Bacterial Single-cell RNA-seq Reveals Biofilm Heterogeneity |
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| Relations |
| BioProject |
PRJNA1081799 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE260457_CC_rRNA_and_mRNA_reads.txt.gz |
112.3 Kb |
(ftp)(http) |
TXT |
| GSE260457_Detailed_Computational_Pipeline.txt.gz |
6.1 Kb |
(ftp)(http) |
TXT |
| GSE260457_ECOLI_rRNA_and_mRNA_reads.txt.gz |
116.9 Kb |
(ftp)(http) |
TXT |
| GSE260457_RAW.tar |
22.2 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE260457_Result_of_correlation_analysis_between_PETRI_and_RiboD-PETRI.xlsx |
115.6 Kb |
(ftp)(http) |
XLSX |
| GSE260457_Result_of_correlation_analysis_between_bulk_and_RiboD-PETRI.xlsx |
117.8 Kb |
(ftp)(http) |
XLSX |
| GSE260457_SA_rRNA_and_mRNA_reads.txt.gz |
71.2 Kb |
(ftp)(http) |
TXT |
| GSE260457_scripts.tar.gz |
10.2 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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