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| Status |
Public on Feb 20, 2024 |
| Title |
PA-biofilm-ΔΔ, replicate 2, scRNA-seq |
| Sample type |
SRA |
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| Source name |
bacterial cell
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| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
cell type: bacterial cell
genotype: WT
treatment: 24 h static biofilm
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RiboD-mSPLiT, all cells were from pure culture in vitro. Cells were harvested by centrifuge;
For RiboD-mSPLiT, library was performed accarding to the Materials and Methods section;
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RiboD-mSPLiT
0122-H
PAO1 rRNA and mRNA reads.txt
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| Data processing |
The demultiplexing, barcodes processing, gene counting and aggregation of scRNA-seq data were made by scripts compiled in Python 2.7.15 as previously described with some modifications. [lattman, W. Jiang, P. Oikonomou, S. Tavazoie, Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature microbiology 5, 1192 (Oct, 2020).]. Downstream analysis of single cell data was performed using pipelines detailed in Seurat v4.3.0.
For corralation analysis of bulk RNA-Seq and scRNA-seq data, scRNA-seq data was combined with the UMI sums of all cells. Single-cell and bulk transcriptomes of E.coli were compared by computing the Pearson correlation of log2 transcripts reads of each gene between the two measurements.
For scRNA-seq data mRNA / total RNA ratio analysis, we removed the barcodes sequence contained in the front, and the interference of the last ten bases, and kept only 20 bases for mapping. Then we mapped the data from the different species to the corresponding reference genomes.
(Detailed codes were saved in "Detailed Computational Pipeline.docx" and "scripts" compressed package .)
Assembly: E.coli MG1655 K12
Supplementary files format and content: matrix files
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data
Supplementary files format and content: tab-delimited files includes raw counts for samples of the same species
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| Submission date |
Jul 28, 2023 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Xiaodan Yan |
| E-mail(s) |
2019206500042@whu.edu.cn
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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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| Platform ID |
GPL28916 |
| Series (2) |
| GSE239504 |
Bacterial single cell RNA-seq unveils cyclic-di-GMP as an antitoxin critical for antibiotic tolerance in biofilm [scRNA-seq] |
| GSE239505 |
Bacterial single cell RNA-seq unveils cyclic-di-GMP as an antitoxin critical for antibiotic tolerance in biofilm. |
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| Relations |
| BioSample |
SAMN36737317 |
| SRA |
SRX21179110 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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