Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30815525", "kind": "science-record", "revision": 7, "content_hash": "sha256:6082d781c1d31c6dd3ea6bc666c21d1254cccf78c4dcba7df8d0733568f89e86", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:00:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.", "doi": "10.1016/j.dib.2019.103701", "pmid": "30815525", "authors": ["Desislava S Makeeva", "Andrey S Lando", "Aleksandra Anisimova", "Artyom A Egorov", "Maria D Logacheva", "Alexey A Penin", "Dmitry E Andreev", "Pavel G Sinitcyn", "Ilya M Terenin", "Ivan N Shatsky", "Ivan V Kulakovskiy", "Sergey E Dmitriev"], "journal": "Data in brief", "year": 2019, "abstract": "TMA20 (MCT-1), TMA22 (DENR) and TMA64 (eIF2D) are eukaryotic translation factors involved in ribosome recycling and re-initiation. They operate with P-site bound tRNA in post-termination or (re-)initiation translation complexes, thus participating in the removal of 40S ribosomal subunit from mRNA stop codons after termination and controlling translation re-initiation on mRNAs with upstream open reading frames (uORFs), as well as de novo initiation on some specific mRNAs. Here we report ribosomal profiling data of S.cerevisiae strains with individual deletions of TMA20, TMA64 or both TMA20 and TMA64 genes. We provide RNA-Seq and Ribo-Seq data from yeast strains grown in the rich YPD or minimal SD medium. We illustrate our data by plotting differential distribution of ribosomal-bound mRNA fragments throughout uORFs in 5'-untranslated region (5' UTR) of GCN4 mRNA and on mRNA transcripts encoded in MAT locus in the mutant and wild-type strains, thus providing a basis for investigation of the role of these factors in the stress response, mating and sporulation. We also document a shift of transcription start site of the APC4 gene which occurs when the neighboring TMA64 gene is replaced by the standard G418-resistance cassette used for the creation of the Yeast Deletion Library. This shift results in dramatic deregulation of the APC4 gene expression, as revealed by our Ribo-Seq data, which can be probably used to explain strong genetic interactions of TMA64 with genes involved in the cell cycle and mitotic checkpoints. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039).", "claims": [{"id": "claim-data-access", "statement": "Analyzed data is presented in the article. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30815525", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Analyzed data is presented in the article. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30815525"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE122039"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE122039"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30815525", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2019.103701", "sha256": "sha256:f0c6d716237376e5e133b15f07ad7eb1a4fce36765df3635892c71eeee75afaf", "bytes": 25278, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2019.103701", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6378902", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE122039", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE122039", "version": null, "note": "Analyzed data is presented in the article. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Analyzed data is presented in the article. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3453486", "GSM3453487", "GSM3453488", "GSM3453489", "GSM3453490", "GSM3453491", "GSM3453492", "GSM3453493", "GSM3453494", "GSM3453495", "GSM3453496", "GSM3453497", "GSM3453498", "GSM3453499", "GSM3453500", "GSM3453501", "GSM3453502", "GSM3453503"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "13821", "taxon": "Saccharomyces cerevisiae", "title": "Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30815525:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:46bea5af0ed40bb825c4d24629b669da8f914c79ad31a7845a61fb296fbb58c6", "bytes": 1213, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t0005", "version": null, "note": "Summary of datasets obtained in the study.", "structure": {"pmcid": "PMC6378902", "section_index": 5, "section_title": "Data", "row_count": 19, "column_count": 6}, "table": {"label": "Table 1", "caption": "Summary of datasets obtained in the study.", "rows": [["Sample", "Sample name", "Yeast strain name", "Yeast strain genotype", "Growth media", "Sample type"], ["1", "wt1_ribo", "wt", "MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0", "YPD", "Ribo-Seq"], ["2", "wt1_rna", "YPD", "RNA-Seq"], ["3", "wt2_ribo", "YPD", "Ribo-Seq"], ["4", "wt2_rna", "YPD", "RNA-Seq"], ["5", "wt_sd_ribo", "SD", "Ribo-Seq"], ["6", "wt_sd_rna", "SD", "RNA-Seq"], ["7", "tma20_ribo", "Δtma20", "MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 tma20Δ:KanMX4", "YPD", "RiboSeq"], ["8", "tma20_rna", "YPD", "RNA-Seq"], ["9", "tma20_sd_ribo", "SD", "Ribo-Seq"], ["10", "tma20_sd_rna", "SD", "RNA-Seq"], ["11", "tma64_ribo", "Δtma64", "MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 tma64Δ:KanMX4", "YPD", "Ribo-Seq"], ["12", "tma64_rna", "YPD", "RNA-Seq"], ["13", "tma64_sd_ribo", "SD", "Ribo-Seq"], ["14", "tma64_sd_rna", "SD", "RNA-Seq"], ["15", "tma20tma64_ribo", "Δtma20Δtma64", "MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 tma64Δ:HygMX4 tma20Δ:KanMX4", "YPD", "Ribo-Seq"], ["16", "tma20tma64_rna", "YPD", "RNA-Seq"], ["17", "tma20tma64_sd_ribo", "SD", "Ribo-Seq"], ["18", "tma20tma64_sd_rna", "SD", "RNA-Seq"]], "row_count": 19, "column_count": 6, "numeric_cells": 37, "header_rows": 1, "locator": "section[5]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE122039 not downloaded", "asset:data:geo:GSE122039 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "read_mapping", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "read mapping"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: read_mapping."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE122039"], "resolved_accessions": ["GSE122039"], "statements": ["Analyzed data is presented in the article. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039)."], "basis": "The paper names GSE122039 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:30815525", "data:geo:GSE122039", "asset:table:pmid:30815525:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE122039"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:56Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22235, "completion_tokens": 855, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30815525", "type": "paper", "label": "pmid:30815525"}, {"id": "source:pmid:30815525", "type": "manuscript", "label": "PMID 30815525 full text"}, {"id": "data:geo:GSE122039", "type": "dataset", "label": "GEO GSE122039"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30815525", "type": "paper", "label": "pmid:30815525"}, {"id": "source:pmid:30815525", "type": "manuscript", "label": "PMID 30815525 full text"}, {"id": "data:geo:GSE122039", "type": "dataset", "label": "GEO GSE122039"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30815525", "type": "extraction", "used": ["source:pmid:30815525"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE122039", "type": "accession_resolution", "used": ["data:geo:GSE122039"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30815525", "parent_hash": "sha256:b3e064c28408dcb8fd60596e627d6fc87b787eebddeef191cca73a3fc658538f", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE122039 licence not read", "asset:data:geo:GSE122039 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D)", "64 or both TMA20 and TMA64 genes. We provide RNA-Seq and Ribo-Seq data from yeast strains grown i", "the cell cycle and mitotic checkpoints. Raw RNA-Seq and Ribo-Seq data as well as all gene counts"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["read mapping"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}