Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484242", "kind": "science-record", "revision": 7, "content_hash": "sha256:26f362f254f5b123dc53daf58980c976055352a70828841b0d9ee428c924f025", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T21:58:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology.", "doi": "10.1016/j.gdata.2015.05.033", "pmid": "26484242", "authors": ["David Lalaouna", "Eric Massé"], "journal": "Genomics data", "year": 2015, "abstract": "RNA sequencing (RNAseq) technology recently allowed the identification of thousands of small RNAs (sRNAs) within the prokaryotic kingdom. However, drawing the comprehensive interaction map of a sRNA remains a challenging task. To address this problem, we recently developed a method called MAPS (MS2 affinity purification coupled with RNA sequencing) to characterize the full targetome of specific sRNAs. This method enabled the identification of target RNAs interacting with sRNAs, regardless of the type of regulation (positive or negative), type of targets (mRNA, tRNA, sRNA) or their abundance. We also demonstrated that we can use this technology to perform a reverse MAPS experiment, where an RNA fragment of interest is used as bait to identify interacting sRNAs. Here, we demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers (ITS) of metZ-metW-metV tRNA transcript, confirming results obtained with MS2-RybB MAPS. Both raw and analyzed RNAseq data are available in GEO database (GSE66517).", "claims": [{"id": "claim-method", "statement": "Here, Read counts were normalized by coverage according to Oshlack et al. [6].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484242", "locator": "sections[8] \"Data processing\" paragraph 3", "quote": "Here, Read counts were normalized by coverage according to Oshlack et al. [6]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Both raw and analyzed RNAseq data are available in GEO database (GSE66517).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484242", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Both raw and analyzed RNAseq data are available in GEO database (GSE66517)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers of the metZ–metW–metV tRNA transcript, confirming results obtained with MS2-RybB MAPS; it identifies MAPS as the method used and states that both raw and analyzed RNAseq data are available in GEO database (GSE66517).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484242", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers (ITS) of metZ–metW–metV tRNA transcript, confirming results obtained with MS2-RybB MAPS."}, {"asset": "source:pmid:26484242", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Both raw and analyzed RNAseq data are available in GEO database (GSE66517)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers of the metZ–metW–metV tRNA transcript, confirming results obtained with MS2-RybB MAPS; it identifies MAPS as the method used and states that both raw and analyzed RNAseq data are available in GEO database (GSE66517).", "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:26484242"], "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:GSE66517"], "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:GSE66517"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484242", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.05.033", "sha256": "sha256:5475ef05406be82826b5fb17175f9f5beff4c92c6d2df87dd274e0700ea31832", "bytes": 6998, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.05.033", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583644", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE66517", "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=GSE66517", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66517", "version": null, "note": "Both raw and analyzed RNAseq data are available in GEO database (GSE66517).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Both raw and analyzed RNAseq data are available in GEO database (GSE66517).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1624356", "GSM1624357"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "19168", "taxon": "Escherichia coli K-12", "title": "Identification of sRNA binding to ITSmetZW and ITSmetWV using MS2-affinity purification coupled with RNA sequencing (MAPS) technology", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484242:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6b928dfb05f72781427e9e934d453b4e12f5509074846e2b3c519904e04c59ad", "bytes": 520, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4583644", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Escherichia coli K12 substrain MG1655"], ["Sex", ""], ["Sequencer or array type", "Illumina Miseq"], ["Data format", "Raw and analyzed"], ["Experimental factors", "MS2 tagged RNA vs. untagged RNA control"], ["Experimental features", "MS2-affinity purification coupled with RNA sequencing"], ["Consent", ""], ["Sample source location", ""]], "row_count": 9, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE66517 not downloaded", "asset:data:geo:GSE66517 licence not read"]}, "analysis": {"state": "partial", "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": "Bowtie"}}, {"id": "method-2", "family": null, "specific": null, "label": "Coverage normalization of read counts", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Here, Read counts were normalized by coverage according to Oshlack et al. [6]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["GSE66517"], "resolved_accessions": ["GSE66517"], "statements": ["Both raw and analyzed RNAseq data are available in GEO database (GSE66517)."], "basis": "The paper names GSE66517 in GEO database 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:26484242", "data:geo:GSE66517", "asset:table:pmid:26484242:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE66517"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:43Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 18810, "completion_tokens": 2243, "cached_tokens": 1960}}, "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:26484242", "type": "paper", "label": "pmid:26484242"}, {"id": "source:pmid:26484242", "type": "manuscript", "label": "PMID 26484242 full text"}, {"id": "data:geo:GSE66517", "type": "dataset", "label": "GEO GSE66517"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484242", "type": "paper", "label": "pmid:26484242"}, {"id": "source:pmid:26484242", "type": "manuscript", "label": "PMID 26484242 full text"}, {"id": "data:geo:GSE66517", "type": "dataset", "label": "GEO GSE66517"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484242", "type": "extraction", "used": ["source:pmid:26484242"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE66517", "type": "accession_resolution", "used": ["data:geo:GSE66517"], "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:26484242", "parent_hash": "sha256:6687d973a4677b0af11899713a9ebc9d6cca40b0bb707e9f7bf28e5622fcdfa1", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE66517 licence not read", "asset:data:geo:GSE66517 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["using MS2-affinity purification coupled with RNA sequencing (MAPS) technology.", "RNA sequencing (RNAseq) technology recently allowed the identificat", "ed with MS2-RybB MAPS. Both raw and analyzed RNAseq data are available in GEO database (GSE66517", "RNA sequencing (RNAseq) technology recently allowed the ide"], "order_basis": "paper_text_order:65", "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": ["Bowtie"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}