{"doi":"10.46471/gigabyte.129","title":"Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis","abstract":"Nanopore direct RNA sequencing (DRS) enables measurements of RNA modifications. Modification-free transcripts are a practical and targeted control for DRS, providing a baseline measurement for canonical nucleotides within a matched and biologically-derived sequence context. However, these controls can be challenging to generate and carry nanopore-specific nuances that can impact analyses. We produced DRS datasets using modification-free transcripts from in vitro transcription of cDNA from six immortalized human cell lines. We characterized variation across cell lines and demonstrated how these may be interpreted. These data will serve as a versatile control and resource to the community for RNA modification analyses of human transcripts.","journal":"Gigabyte","year":2024,"id":430425,"datarank":0.7134600434459131,"base_score":2.995732273553991,"endowment":2.995732273553991,"self_citation_contribution":0.4493598410330987,"citation_network_contribution":0.2641002024128144,"self_endowment_contribution":0.4493598410330987,"citer_contribution":0.2641002024128144,"corpus_percentile":71.90376730873366,"corpus_rank":3633,"citation_count":19,"citer_count":13,"citers_with_citation_signal":11,"citers_with_endowment":11,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7067,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1162299,"name":"Stuart Akeson","orcid":"0009-0008-8008-2486","position":1,"is_corresponding":false},{"id":807910,"name":"Sepideh Tavakoli","orcid":"0000-0002-0802-7051","position":2,"is_corresponding":false},{"id":1162300,"name":"Dylan Bloch","orcid":"0000-0002-5382-5765","position":3,"is_corresponding":false},{"id":1162301,"name":"Isabel N. Klink","orcid":"0009-0002-9567-8158","position":4,"is_corresponding":false},{"id":109466,"name":"Miten Jain","orcid":"0000-0002-4571-3982","position":5,"is_corresponding":false},{"id":807912,"name":"Sara H. Rouhanifard","orcid":"0000-0002-6991-4877","position":6,"is_corresponding":false},{"id":807911,"name":"Caroline A. McCormick","orcid":"0009-0000-0670-6707","position":0,"is_corresponding":true}],"reference_count":26,"raw_metadata":null,"created_at":"2026-07-19T01:59:16.092672Z","pmid":"38962390","pmcid":"PMC11221353","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":50.0,"fair_a":37.5,"fair_i":80.0,"fair_r":41.6667,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","grounded":false,"rationale":"The paper provides a persistent identifier in the form of a BioProject accession (PRJNA947135), which is a PID scheme. 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FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","grounded":false,"rationale":"The data availability statement points to repositories with accessions and DOIs, fulfilling Colavizza category 3. 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[majority verdict 'yes' (3/5 passes agreed)]","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":0.5,"verdict":"partial","evidence":"Basecalled reads were aligned with minimap2 (v2.24) to the GRCh38.p10 reference genome and Gencode.v45 transcript sequences.","grounded":false,"rationale":"The paper names GENCODE (v45) and GRCh38.p10, which are community-standard reference annotations and genome assemblies. 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[majority verdict 'yes' (4/5 passes agreed)]","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":41.67,"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 explicitly state a reuse license for the dataset; only the article's CC-BY license is mentioned, which applies to the text, not the data.","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":"DRS runs were base called with Guppy v6.4.2 (RRID:SCR_023196) using the high accuracy model and the default basecalling quality-score filter Q ≥ 7","grounded":true,"rationale":"The paper names specific software (Guppy with version) used to produce the data. 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For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","why":"The paper provides a persistent identifier in the form of a BioProject accession (PRJNA947135), which is a PID scheme. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","why":"The paper names NIH NCBI-SRA (a repository listed in re3data/FAIRsharing) as the holder of the data. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","why":"The sentence states unconditional public availability of the data 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. 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Additional data and code snapshots are in Zenodo [28] and GigaDB [24]. FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","why":"The data availability statement points to repositories with accessions and DOIs, fulfilling Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. 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 observed 17,038 unique genes aligned with at least one DRS read from the panIVT comprising 85.69% of all human protein-coding genes in Gencode v45.","why":"The dataset's content is described in running prose rather than an itemized inventory, table, or section heading listing files or variables. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"FASTQ files and Fast5 raw data generated in this work have been made publicly available in NIH NCBI-SRA under the BioProject accession PRJNA947135.","why":"The paper uses the phrase 'publicly available' which is a natural-language synonym for open access. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. 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[majority verdict 'no' (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.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list."],"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":"2026-07-20T11:55:40.913140Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}