← All .science files
pmid:26484245
Transcriptional profiling of CcpE-regulated genes in Staphylococcus aureus.
Han Li · Yue Ding · Lefu Lan
Genomics data · 2015 doi:10.1016/j.gdata.2015.06.005
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 3 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
[2] object · 6 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 6 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484245", "kind": "science-record", "revision": 3, "content_hash": "sha256:9da76c6f3e954f92f6e9a34e8bd3d60a998f3256da29c7d807d8414ab0b6519c", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T21:20:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptional profiling of CcpE-regulated genes in Staphylococcus aureus.", "doi": "10.1016/j.gdata.2015.06.005", "pmid": "26484245", "authors": ["Han Li", "Yue Ding", "Lefu Lan"], "journal": "Genomics data", "year": 2015, "abstract": "The transcriptional regulator CcpE is an important citrate-sensing regulator that modulates metabolic state, virulence factor expression, and bacterial virulence of Staphylococcus aureus (Ding et al., 2014 [1]). In this article, we report detailed methods for genome-wide transcriptional profiling of CcpE-regulated genes generated for the research article \"Metabolic sensor governing bacterial virulence in Staphylococcus aureus\" (Ding et al., 2014 [1]). All transcriptional profiling data was deposited to Gene Expression Omnibus (GEO) database under accession number GSE57260.", "claims": [{"id": "claim-method", "statement": "Gene expression analysis was performed using three biological replicate mRNA samples for each strain which were analyzed with SAM (Significance Analysis of Microarrays) software [8].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484245", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "Gene expression analysis was performed using three biological replicate mRNA samples for each strain which were analyzed with SAM (Significance Analysis of Microarrays) software [8]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All transcriptional profiling data was deposited to Gene Expression Omnibus (GEO) database under accession number GSE57260.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484245", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All transcriptional profiling data was deposited to Gene Expression Omnibus (GEO) database under accession number GSE57260."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports methods for genome-wide transcriptional profiling of CcpE-regulated genes, using SAM for differential-expression analysis and depositing the raw and analyzed data in GEO under accession GSE57260.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484245", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this article, we report detailed methods for genome-wide transcriptional profiling of CcpE-regulated genes generated for the research article “Metabolic sensor governing bacterial virulence in Staphylococcus aureus” (Ding et al., 2014 [1])."}, {"asset": "source:pmid:26484245", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "Gene expression analysis was performed using three biological replicate mRNA samples for each strain which were analyzed with SAM (Significance Analysis of Microarrays) software [8]."}, {"asset": "source:pmid:26484245", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "Raw data files were also deposited on GEO under the accession number GSE57260."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports methods for genome-wide transcriptional profiling of CcpE-regulated genes, using SAM for differential-expression analysis and depositing the raw and analyzed data in GEO under accession GSE57260.", "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:26484245"], "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:GSE57260"], "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:GSE57260"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484245", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.06.005", "sha256": "sha256:7d2f851a8d7d535fc562962f27bee90051dd96547fa8c40ece55e93d94053270", "bytes": 7189, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.06.005", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583652", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57260", "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=GSE57260", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57260", "version": null, "note": "All transcriptional profiling data was deposited to Gene Expression Omnibus (GEO) database under accession number GSE57260.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All transcriptional profiling data was deposited to Gene Expression Omnibus (GEO) database under accession number GSE57260.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1378046", "GSM1378047", "GSM1378048", "GSM1378049", "GSM1378050", "GSM1378051"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "1339", "taxon": "Staphylococcus aureus; Staphylococcus aureus subsp. aureus str. Newman", "title": "Transcriptome of the NWMN_0641 deletion mutant strain and the wild-type Staphylococcus aureus Newman strain", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE57260 not downloaded", "asset:data:geo:GSE57260 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "SAM (Significance Analysis of Microarrays)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Gene expression analysis was performed using three biological replicate mRNA samples for each strain which were analyzed with SAM (Significance Analysis of Microarrays) software [8]."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (SAM (Significance Analysis of Microarrays)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE57260"], "resolved_accessions": ["GSE57260"], "statements": ["All transcriptional profiling data was deposited to Gene Expression Omnibus (GEO) database under accession number GSE57260."], "basis": "The paper names GSE57260 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484245", "data:geo:GSE57260"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE57260"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:45Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 19968, "completion_tokens": 1973, "cached_tokens": 1936}}, "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:26484245", "type": "paper", "label": "pmid:26484245"}, {"id": "source:pmid:26484245", "type": "manuscript", "label": "PMID 26484245 full text"}, {"id": "data:geo:GSE57260", "type": "dataset", "label": "GEO GSE57260"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484245", "type": "paper", "label": "pmid:26484245"}, {"id": "source:pmid:26484245", "type": "manuscript", "label": "PMID 26484245 full text"}, {"id": "data:geo:GSE57260", "type": "dataset", "label": "GEO GSE57260"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484245", "type": "extraction", "used": ["source:pmid:26484245"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE57260", "type": "accession_resolution", "used": ["data:geo:GSE57260"], "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:26484245", "parent_hash": "sha256:74e757ef9924cb554c77ef80a45a5788761595964570482fa39f08011b8d7ee6", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE57260 licence not read", "asset:data:geo:GSE57260 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}