5PSeq Explorer Data Freeze

Vicent Pelechano

doi:10.48723/zchv-5x22

5PSeq Explorer Data Freeze

https://doi.org/10.48723/zchv-5x22

This data freeze accompanies 5PSeq Explorer and it contains 775 5PSeq datasets compiled from 18 published studies interrogating various aspects of biology at the interface of mRNA decay and translation, including both genetic and environmental perturbations. To enable comparability across conditions and cross-species we processed all data uniformly (see Methods). The generated database consists of: (1) metadata, (2) raw processed counts files of amino acid, codon, frame preferences, metagene counts around start and termination sites, additional count files as documented on the Fivepseq package output documentation, and (3) RNA composition. For Eukaryotes, the collection consists of 378 yeast samples (Ascomycota phylum) with an overrepresentation for Saccharomyces cerevisiae (n= 340). For bacteria, we provide 397 samples across Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota and Verrucomicrobiota phyla with an overreprepresentation for Bacillus subtilis (n= 67) and Aggregatibacter actinomycetemcomitans (n=59).

Download data and documentation (3 files / 2.56 GiB)

Data files

5PSeqExplorer-Data.tar.gz
2.56 GiB
5PSeqExplorer-Data.tar.gz.sha256
92 Bytes

Documentation files

README.txt
13.34 KiB

Citation and access

Data access level:

Data are openly accessible

Creator/Principal investigator(s):

Irene Stevens - Karolinska Universitet - Department of Microbiology, Tumor and Cell Biology [C1]
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ORCIDOpens in a new tab
Vicent Pelechano - Karolinska Institutet - Department of Microbiology, Tumor and Cell Biology [C1]
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ORCIDOpens in a new tab

Research principal:

Karolinska Institutet
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ROROpens in a new tab

Data contains personal data:

Citation:

License:

Creative Commons Public Domain Dedication (CC0 1.0)Opens in a new tab

Language:

English

Method and outcome

Unit of analysis:

Cells

Population:

Molecular data (775 5PSeq datasets) collected from 18 published studies interrogating various mRNA decay and translation across genetic and environmental perturbations. For Eukaryotes, the collection consists of 378 yeast samples (Ascomycota phylum) with an overrepresentation of Saccharomyces cerevisiae (n= 340). For bacteria we provide 397 samples across Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota and Verrucomicrobiota phyla with an overreprepresentation for Bacillus subtilis (n= 67) and Aggregatibacter actinomycetemcomitans (n=59).

Time method:

Other

Study design:

Preclinical study

Description of study design:

Compiled public sequencing datasets

Sampling procedure:

Other

Description of sampling:

A collection of published molecular data was uniformly processed and relies on sampling carried out by the original study.

Time period(s) investigated:

2015 - 2024

Variables:

Number of individuals/objects:

775

Data format/data structure:

Numeric
Text

Data collection - Experiment

Mode of collection:

Experiment

Description of the mode of collection:

Data collection information for each record is available in the metadata file attached. The library preparation protocol for 5Pseq, and the version of the protocol used, is noted in the metadata (attached file). All records are accompanied by a GEO_ID, SRA_ID and PubMed ID for a detailed record of the biosample, collection and experimental details.

Time period(s) for data collection:

2015 - 2024

Data collector:

Karolinska Institutet
Opens a new window at ror.org.
ROROpens in a new tab

Sample size:

775

Source of the data:

Research data
Research data: Published

Instrument

Name:

Illumina NextSeq 2000

Type:

Technical instrument(s)

Name:

Illumina NextSeq 500

Type:

Technical instrument(s)

Name:

Illumina NovaSeq 6000

Type:

Technical instrument(s)

Name:

Illumina HiSeq 2000

Type:

Technical instrument(s)

Name:

Illumina MiSeq

Type:

Technical instrument(s)

Administrative information

Responsible department/unit:

Department of Microbiology, Tumor and Cell Biology [C1]

Commissioning organisation:

Karolinska Institutet
Opens a new window at ror.org.
ROROpens in a new tab

Funding

Funding agency:

Swedish Research Council
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ROROpens in a new tab

Award number:

VR 2021-06112, 2022-05272, 2023-02026 and 2024-03210

Funding agency:

Wallenberg Academy Fellowship
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ROROpens in a new tab

Award number:

2021.0167

Funding agency:

Karolinska Institutet
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ROROpens in a new tab

Award number:

SciLifeLab, SFO, KID and KI funds

Topic and keywords

CESSDA Topic Classification:

Science and technology
Biotechnology

Standard för svensk indelning av forskningsämnen 2025:

Medical and health sciences
Medical genetics and genomics
Cell and molecular biology

Keywords:

Investigative techniques
Gene expression profiling
Rna
Rna sequencing

Relations

Homepage:

https://fivepseq-explorer.serve.scilifelab.se/app/fivepseq-explorerOpens in a new tab

Is documented by:

https://5pseq-explorer-docs.readthedocs.io/en/latest/index.htmlOpens in a new tab

Is derived from:

https://github.com/irenestevens8/5Pseq-ExplorerOpens in a new tab

Publications

Citation:

Allen, G., Weiss, B., Panasenko, O. O., Huch, S., Villanyi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. E., Corden, J., Polte, C., Shore, D., Ignatova, Z., Pelechano, V., & Collart, M. A. (2023). Not1 and Not4 inversely determine mRNA solubility tol.bhat sets the dynamics of co-translational events. Genome Biology, 24(1), 30. https://doi.org/10.1186/s13059-023-02871-7Opens in a new tab

DOI:
10.1186/s13059-023-02871-7Opens in a new tab

Citation:

Pelechano, V., Wei, W., & Steinmetz, L. M. (2015). Widespread Co-translational RNA Decay Reveals Ribosome Dynamics. Cell, 161(6), 1400–1412. https://doi.org/10.1016/j.cell.2015.05.008Opens in a new tab

DOI:
10.1016/j.cell.2015.05.008Opens in a new tab

Citation:

Zhang, Y., & Pelechano, V. (2021). Application of high-throughput 5’P sequencing for the study of co-translational mRNA decay. In STAR PROTOCOLS (Vol. 2, Issue 2, pp. 100447–100447). https://doi.org/10.1016/j.xpro.2021.100447Opens in a new tab

DOI:
10.1016/j.xpro.2021.100447Opens in a new tab

SwePub:

oai:swepub.ki.se:462699Opens in a new tab

Citation:

Pelechano, V., & Alepuz, P. (2017). eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences. In NUCLEIC ACIDS RESEARCH (Vol. 45, Issue 12, pp. 7326–7338). https://doi.org/10.1093/nar/gkx479Opens in a new tab

DOI:
10.1093/nar/gkx479Opens in a new tab

SwePub:

oai:swepub.ki.se:496546Opens in a new tab

Citation:

Wei, W., Hennig, B., Wang, J., Zhang, Y., Piazza, I., Sanchez, Y., Chabbert, C., Adjalley, S., Steinmetz, L., & Pelechano, V. (2019). Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast. In GENOME RESEARCH (Vol. 29, Issue 12, pp. 1974–1984). https://doi.org/10.1101/gr.243378.118Opens in a new tab

DOI:
10.1101/gr.243378.118Opens in a new tab

SwePub:

oai:swepub.ki.se:475566Opens in a new tab

Citation:

Huch, S., Nersisyan, L., Ropat, M., Barrett, D., Wu, M., Wang, J., Valeriano, V., Vardazaryan, N., Huerta-Cepas, J., & Wei, W. (2023). Atlas of mRNA translation and decay for bacteria. In NATURE MICROBIOLOGY (Vol. 8, Issue 6, pp. 1123–1136). https://doi.org/10.1038/s41564-023-01393-zOpens in a new tab

DOI:
10.1038/s41564-023-01393-zOpens in a new tab

SwePub:

oai:swepub.ki.se:445890Opens in a new tab

Citation:

Jordan-Pla, A., Zhang, Y., Garcia-Martinez, J., Chattopadhyay, S., Forte, A., Choder, M., Pelechano, V., & Perez-Ortin, J. (2025). Proper 5′-3′ cotranslational mRNA decay in yeast requires import of Xrn1 to the nucleus. In PLOS ONE (Vol. 20, Issue 1, pp. e0308195–e0308195). https://doi.org/10.1371/journal.pone.0308195Opens in a new tab

DOI:
10.1371/journal.pone.0308195Opens in a new tab

SwePub:

oai:swepub.ki.se:901940Opens in a new tab

Citation:

Zeng, F., Li, X., Pires-Alves, M., Chen, X., Hawk, C. W., & Jin, H. (2021). Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Cell Reports, 37(4), 109877. https://doi.org/10.1016/j.celrep.2021.109877Opens in a new tab

DOI:
10.1016/j.celrep.2021.109877Opens in a new tab

Citation:

Rodriguez-Galan, O., Garcia-Gomez, J., Rosado, I., Wei, W., Mendez-Godoy, A., Pillet, B., Alekseenko, A., Steinmetz, L., Pelechano, V., & Kressler, D. (2020). A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. In NUCLEIC ACIDS RESEARCH (Vol. 49, Issue 1, pp. 206–220). https://doi.org/10.1093/nar/gkaa1200Opens in a new tab

DOI:
10.1093/nar/gkaa1200Opens in a new tab

SwePub:

oai:swepub.ki.se:465782Opens in a new tab

Citation:

Zhang, Y., Nersisyan, L., Fürst, E., Alexopoulos, I., Santolaria, C., Huch, S., Bassot, C., Garre, E., Sunnerhagen, P., Piazza, I., & Pelechano, V. (2025). Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decay. In Molecular Cell (Vol. 85, Issue 10). https://doi.org/10.1016/j.molcel.2025.04.022Opens in a new tab

DOI:
10.1016/j.molcel.2025.04.022Opens in a new tab

SwePub:

oai:gup.ub.gu.se/350230Opens in a new tab

Citation:

Stevens, I., Silao, F.-G. S., Huch, S., Liu, H., Ryman, K., Carvajal-Jimenez, A., Ljungdahl, P., & Pelechano, V. (2024). The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans. In Scientific Reports (No. 29012; Vol. 14, Issue 1). https://doi.org/10.1038/s41598-024-80435-wOpens in a new tab

URN:
urn:nbn:se:su:diva-240803Opens in a new tab
DOI:
10.1038/s41598-024-80435-wOpens in a new tab

SwePub:

oai:DiVA.org:su-240803Opens in a new tab

Citation:

Turnbull, K., Paternoga, H., von, der W. E., Egorov, A., Pochopien, A., Zhang, Y., Nersisyan, L., Margus, T., Johansson, M., & Pelechano, V. (2024). The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site. In BIORXIV. https://doi.org/10.1101/2024.05.29.596377Opens in a new tab

DOI:
10.1101/2024.05.29.596377Opens in a new tab

SwePub:

oai:swepub.ki.se:871626Opens in a new tab

Citation:

Allen, G., Panasenko, O., Villanyi, Z., Zagatti, M., Weiss, B., Pagliazzo, L., Huch, S., Polte, C., Zahoran, S., & Hughes, C. (2021). Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A. In CELL REPORTS (Vol. 36, Issue 9, pp. 109633–109633). https://doi.org/10.1016/j.celrep.2021.109633Opens in a new tab

DOI:
10.1016/j.celrep.2021.109633Opens in a new tab

SwePub:

oai:swepub.ki.se:459365Opens in a new tab

Citation:

Garre, E., Pelechano, V., Sánchez Del Pino, M., Alepuz, P., & Sunnerhagen, P. (2018). The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock. PLoS Genetics, 14(7), e1007563. https://doi.org/10.1371/journal.pgen.1007563Opens in a new tab

DOI:
10.1371/journal.pgen.1007563Opens in a new tab

Citation:

da, S. P., Zhang, Y., Theodorakis, E., Martens, L., Yepez, V., Pelechano, V., & Gagneur, J. (2024). Cellular energy regulates mRNA degradation in a codon-specific manner. In MOLECULAR SYSTEMS BIOLOGY (Vol. 20, Issue 5, pp. 506–520). https://doi.org/10.1038/s44320-024-00026-9Opens in a new tab

DOI:
10.1038/s44320-024-00026-9Opens in a new tab

SwePub:

oai:swepub.ki.se:852942Opens in a new tab

Citation:

Zhang, Y., & Pelechano, V. (2021). High-throughput 5’P sequencing enables the study of degradation-associated ribosome stalls. In CELL REPORTS: METHODS (Vol. 1, Issue 1, pp. 100001–100001). https://doi.org/10.1016/j.crmeth.2021.100001Opens in a new tab

DOI:
10.1016/j.crmeth.2021.100001Opens in a new tab

SwePub:

oai:swepub.ki.se:453805Opens in a new tab

Citation:

Tseng, S. C. (2019). Regulation of RNA Synthesis and Decay via the C-terminal Domain of Pol II. https://asset.library.wisc.edu/1711.dl/52QPBQLOXUAEI8C/R/file-ae24a.pdfOpens in a new tab

Contact

Irene Stevensirene.stevens@ki.seOpens in a new tab

Metadata

Selected format to export the metadata

Version 1

5PSeq Explorer Data Freeze

Data files

Documentation files

Citation and access

Data access level:

Creator/Principal investigator(s):

Research principal:

Data contains personal data:

Citation:

License:

Language:

Method and outcome

Unit of analysis:

Population:

Time method:

Study design:

Description of study design:

Sampling procedure:

Description of sampling:

Time period(s) investigated:

Variables:

Number of individuals/objects:

Data format/data structure:

Data collection - Experiment

Mode of collection:

Description of the mode of collection:

Time period(s) for data collection:

Data collector:

Sample size:

Source of the data:

Instrument

Name:

Type:

Name:

Type:

Name:

Type:

Name:

Type:

Name:

Type:

Administrative information

Responsible department/unit:

Commissioning organisation:

Funding

Funding agency:

Award number:

Funding agency:

Award number:

Funding agency:

Award number:

Topic and keywords

CESSDA Topic Classification:

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Relations

Homepage:

Is documented by:

Is derived from:

Publications

Citation:

DOI:

Citation:

DOI:

Citation:

DOI:

SwePub:

Citation:

DOI:

SwePub:

Citation:

DOI:

SwePub:

Citation:

DOI:

SwePub:

Citation:

DOI:

SwePub:

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