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).
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
Research principal:
Data contains personal data:
No
Citation:
Language:
Method and outcome
Method and outcome
Unit of analysis:
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:
Study design:
- Preclinical study
Description of study design:
Compiled public sequencing datasets
Sampling procedure:
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:
Variables:
18
Number of individuals/objects:
775
Data collection - Experiment
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
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Sample size:
775
Source of the data:
- Research data
- Research data: Published
Instrument
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
Administrative information
Responsible department/unit:
Department of Microbiology, Tumor and Cell Biology [C1]
Commissioning organisation:
- Karolinska Institutet
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Funding
Funding
Funding agency:
- Swedish Research Council
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Award number:
VR 2021-06112, 2022-05272, 2023-02026 and 2024-03210
Funding agency:
- Wallenberg Academy Fellowship
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Award number:
2021.0167
Funding agency:
- Karolinska Institutet
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Award number:
SciLifeLab, SFO, KID and KI funds
Topic and keywords
Topic and keywords
CESSDA Topic Classification:
Standard för svensk indelning av forskningsämnen 2025:
Publications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
