{"doi":"10.1128/msystems.00816-22","title":"A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon","abstract":"While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net).","journal":"mSystems","year":2023,"id":358280,"datarank":0.449807987897216,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.07707199042901584,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.07707199042901584,"corpus_percentile":58.11866635723679,"corpus_rank":5415,"citation_count":11,"citer_count":7,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.691,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.21936396.v2"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":148312,"name":"Ulrike Kusebauch","orcid":"0000-0001-6162-7577","position":1,"is_corresponding":false},{"id":268001,"name":"Lívia S. Zaramela","orcid":"0000-0002-1065-3799","position":2,"is_corresponding":false},{"id":705124,"name":"Wei‐Ju Wu","orcid":"0000-0002-0022-2602","position":3,"is_corresponding":false},{"id":989280,"name":"João Paulo P. de Almeida","orcid":"0000-0001-7532-8420","position":4,"is_corresponding":false},{"id":441561,"name":"Serdar Turkarslan","orcid":"0000-0003-1679-6405","position":5,"is_corresponding":false},{"id":441559,"name":"Adrián López García de Lomana","orcid":"0000-0002-9748-347X","position":6,"is_corresponding":false},{"id":989281,"name":"José Vicente Gomes‐Filho","orcid":"0000-0001-5289-8260","position":7,"is_corresponding":false},{"id":989282,"name":"Ricardo Z. N. Vêncio","orcid":"0000-0003-0425-7877","position":8,"is_corresponding":false},{"id":78845,"name":"Robert L. Moritz","orcid":"0000-0002-3216-9447","position":9,"is_corresponding":false},{"id":989283,"name":"Tie Koide","orcid":"0000-0003-4760-2423","position":10,"is_corresponding":false},{"id":400246,"name":"Nitin S. Baliga","orcid":"0000-0001-9157-5974","position":11,"is_corresponding":false},{"id":441562,"name":"Alan P. R. Lorenzetti","orcid":"0000-0002-0291-248X","position":0,"is_corresponding":true}],"reference_count":115,"raw_metadata":null,"created_at":"2026-07-19T01:13:43.629667Z","pmid":"36912639","pmcid":"PMC10134880","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":66.6667,"fair_a":56.25,"fair_i":60.0,"fair_r":33.3333,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":66.67,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Raw DNA-Seq data (FAST5 format) are available at Zenodo (accession number 6303948 [https://doi.org/10.5281/zenodo.6303948]).","grounded":true,"rationale":"The paper provides a DOI (10.5281/zenodo.6303948) for its own data, which is a persistent identifier. 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[majority verdict 'partial' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"FASTQ format","grounded":true,"rationale":"The paper states that the data are in FASTQ format, which is an open, community-standard format.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community standard for data or metadata (e.g., MIAME, MIxS) is named. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"GSE45988","grounded":true,"rationale":"The paper gives an identifier for a third-party dataset (GEO accession) that it used.","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state a reuse licence for the data; only the article's licence is given.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"MiSeq instrument","grounded":true,"rationale":"The paper names specific instruments and platforms used to generate the data, such as the MiSeq instrument. 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[majority verdict 'no' (2/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The code used in this study is available on GitHub in multiple repositories","grounded":false,"rationale":"A machine-resolvable locator (GitHub) is given for the study's own code. 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For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"SmAP1 RIP-Seq raw data (FASTQ format) and DNA-Seq data (demultiplexed, base called, and trimmed) (FASTQ format) were deposited in the NCBI Sequence Read Archive and are publicly available under BioProject accession number PRJNA808788.","why":"The data are deposited in public repositories with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"BioProject accession number PRJNA808788","why":"The dataset identifier appears only in the body text (data availability section), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The code used in this study is available on GitHub in multiple repositories","why":"A machine-resolvable locator (GitHub) is given for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is provided for the dataset; the DOIs may be versioned but not stated. [majority verdict 'no' (2/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"SmAP1 RIP-Seq raw data (FASTQ format) and DNA-Seq data (demultiplexed, base called, and trimmed) (FASTQ format) were deposited in the NCBI Sequence Read Archive and are publicly available under BioProject accession number PRJNA808788. Raw DNA-Seq data (FAST5 format) are available at Zenodo (accession number 6303948 [https://doi.org/10.5281/zenodo.6303948]). 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Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"we compiled the corresponding quantities of mRNAs (RNA-Seq), ribosome-protected mRNA fragments (RPFs) (Ribo-Seq) (43), and proteins (SWATH-MS) (Kusebauch et al., unpublished) for 2,579 genes across the early exponential (TP1), mid-exponential (TP2), late exponential (TP3), and stationary (TP4) phases of growth in batch culture","why":"The dataset's content and extent are described in running prose, not in an itemised inventory. 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[majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object (README, codebook) is named as travelling with the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not human-subject or sensitive data; no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"are publicly available","why":"The paper states the data are available now but does not mention how long they persist. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:21:17.018437Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}