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Persistent Identifier
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doi:10.18710/EGMHAC |
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Publication Date
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2026-04-07 |
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Title
| Replication Data for: Petrisnake, an improved computational pipeline for bacterial single-cell RNA-seq |
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Author
| Pettersen, Jakob Pederhttps://ror.org/00wge5k78ORCIDhttps://orcid.org/0000-0002-3485-1634 |
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Point of Contact
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Use email button above to contact.
Pettersen, Jakob Peder (UiT The Arctic University of Norway)
UiT Research Data Support |
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Description
| In the paper Petrisnake, an improved computational pipeline for bacterial single-cell RNA-seq , two secondary analysis bioinformatic pipelines for data from the PETRI-seq protocol (Blattman et al. 2020) are compared and benchmarked. One of these pipelines is the original PETRI-seq pipeline (Blattman et al. 2020 and Blattman et al. 2024, available at https://github.com/tavalab/PETRI-seq-persistence) and the other is Petrisnake which is introduced by this paper (available at https://github.com/yaccos/Petrisnake and https://workflowhub.eu/workflows/2081).
The benchmarking was conducted on a PETRI-seq sample of exponential phase Escherichia coli cells (Yan et al. 2024), available at NCBI under accession under SRR28148450. Because of size considerations, this raw sequence data are not attached to this repository and must hence be downloaded separately if you want to re-run the benchmarks.
This repository contains the output data files such as gene count matrices and UMI count tables from the two pipelines, in addition to the logs generated. These files are kept as-is with selected figure provided in archive-friendly formats.
For comparing the results of the two pipelines, the paper includes a multi-panel figure comparing the outputs of the two pipelines (comparison.pdf). This repository contains an R script which uses the output data from the pipelines and generates the said figure. (2026-03-20) |
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Subject
| Medicine, Health and Life Sciences |
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Keyword
| Computational Biology http://id.nlm.nih.gov/mesh/D019295 (MeSH) https://www.nlm.nih.gov/mesh/meshhome.html
Single-Cell Gene Expression Analysis https://id.nlm.nih.gov/mesh/D000092386.html (MeSH) https://www.nlm.nih.gov/mesh/meshhome.html
Single-Cell Analysis https://id.nlm.nih.gov/mesh/D059010.html (MeSH) https://www.nlm.nih.gov/mesh/meshhome.html
Escherichia coli https://id.nlm.nih.gov/mesh/D004926.html (MeSH) https://www.nlm.nih.gov/mesh/meshhome.html
Drug Resistance, Microbial https://id.nlm.nih.gov/mesh/D004352.html (MeSH) https://www.nlm.nih.gov/mesh/meshhome.html |
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Related Publication
| Is Supplement To: Pettersen, J. P. and Holsø, Einar. Petrisnake, an improved computational pipeline for bacterial single-cell RNA-seq. Submitted for review
Cites: Blattman, S.B., Jiang, W., McGarrigle, E.R. et al. Identification and genetic dissection of convergent persister cell states. Nature 636, 438–446 (2024). https://doi.org/10.1038/s41586-024-08124-2 doi 10.1038/s41586-024-08124-2 https://doi.org/10.1038/s41586-024-08124-2
Cites: Blattman, S.B., Jiang, W., Oikonomou, P. et al. Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nat Microbiol 5, 1192–1201 (2020). https://doi.org/10.1038/s41564-020-0729-6 doi 10.1038/s41564-020-0729-6 https://doi.org/10.1038/s41564-020-0729-6
Cites: Xiaodan Yan, Hebin Liao, Chenyi Wang, Chun Huang, Wei Zhang, Chunming Guo, Yingying Pu (2024) An improved bacterial single-cell RNA-seq reveals biofilm heterogeneity eLife 13:RP97543 https://doi.org/10.7554/eLife.97543.4 doi 10.7554/eLife.97543.4 https://doi.org/10.7554/eLife.97543.4 |
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Language
| English |
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Producer
| UiT The Arctic University of Norway (UiT) https://en.uit.no/ |
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Contributor
| Supervisor: Holsbø, Einar |
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Funding Information
| Centre for New Antibacterial Strategies at UiT The Artic University of Norway |
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Distributor
| UiT The Arctic University of Norway (UiT) https://dataverse.no/dataverse/uit |
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Depositor
| Pettersen, Jakob Peder |
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Deposit Date
| 2026-03-20 |
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Date of Collection
| Start Date: 2025-01-01; End Date: 2025-03-01 |
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Data Type
| Source code and output of bioinformatic pipelines |
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Software
| Petrisnake, Version: 2.0
PETRI-seq pipeline, Version: v2 |
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Related Material
| The raw data sequence data used for this benchmark (NCBI SRR28148450, see Related Dataset) is a supplement to the paper:
Xiaodan Yan, Hebin Liao, Chenyi Wang, Chun Huang, Wei Zhang, Chunming Guo, Yingying Pu (2024) An improved bacterial single-cell RNA-seq reveals biofilm heterogeneity eLife 13:RP97543 https://doi.org/10.7554/eLife.97543.4 |
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Related Dataset
| Raw data sequence data to generate the results are available at NCBI SRR28148450 (GSM8117655), available at https://www.ncbi.nlm.nih.gov/sra/SRR28148450, submitted by Medical Research Institute, Wuhan University, part of project An Improved Bacterial Single-cell RNA-seq Reveals Biofilm Heterogeneity [scRNA-seq] (PRJNA1081799)
However, these raw sequences are not included because of the sheer size of this data. |
