← All .science files
pmid:26484196
Contribution of nuclear actin to transcription regulation.
Shota Yamazaki · Koji Yamamoto · Masahiko Harata
Genomics data · 2015 doi:10.1016/j.gdata.2015.04.009
Paper
complete
Experiment
complete
Data
partial
Analysis
absent
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 · 1 item
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 · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 2 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 1 item
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
gaps array · 2 items
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 · 3 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 · 8 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484196", "kind": "science-record", "revision": 5, "content_hash": "sha256:24a17120dc4e8568a84f41fc7af3c9ef03daf34c06f8240ccd30e17b4fc78136", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T18:47:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Contribution of nuclear actin to transcription regulation.", "doi": "10.1016/j.gdata.2015.04.009", "pmid": "26484196", "authors": ["Shota Yamazaki", "Koji Yamamoto", "Masahiko Harata"], "journal": "Genomics data", "year": 2015, "abstract": "Actin, an integral component of the cytoskeleton, plays crucial roles in a variety of cell functions, including cell migration, adhesion, polarity and shape change. Studies performed during the last couple of decades have revealed that the actin also exists in the nucleus. However, the function and properties of nuclear actin remained elusive so far. Recently, we showed that an actin tagged with EYFP and fused with a nuclear localization signal (EYFP-NLS-actin) formed visible filamentous (F)-actin bundles in cells. To obtain further details about the individual genes that are affected by the nuclear actin, we have used the microarray analysis to determine the changes in the expression levels of RNAs in HeLa cells as a result of EYFP-NLS-actin expression. Our results suggest that the nuclear actin plays a role in the activation of genes rather than their repression. The data has been deposited in the Gene Expression Omnibus (GEO) database under the accession number GSE59799.", "claims": [{"id": "claim-data-access", "statement": "The data has been deposited in the Gene Expression Omnibus (GEO) database under the accession number GSE59799.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484196", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data has been deposited in the Gene Expression Omnibus (GEO) database under the accession number GSE59799."}], "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:26484196"], "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:GSE59799"], "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:GSE59799"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484196", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.04.009", "sha256": "sha256:dad8712c4dac831f4402878763133f86ec28f7c4fd681162528fa069368858c5", "bytes": 5995, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.04.009", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4536027", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59799", "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=GSE59799", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59799", "version": null, "note": "The data has been deposited in the Gene Expression Omnibus (GEO) database under the accession number GSE59799.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data has been deposited in the Gene Expression Omnibus (GEO) database under the accession number GSE59799.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1446588", "GSM1446589"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Nuclear actin activates human transcription factor genes including the OCT4 gene", "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:26484196:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6dc369fcfb89ebb04598c074b99dd51e6334d55ca1440ac6ea1aee6a1646f6a4", "bytes": 715, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4536027", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Human/HeLa cell line"], ["Sex", "female"], ["Sequencer or array type", "Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version)"], ["Data format", "Raw data"], ["Experimental factors", "HeLa cells expressing EYFP-actin or EYFP-NLS-actin"], ["Experimental features", "RNAs prepared from EYFP-actin and EYFP-NLS-actin expressing HeLa cells, which were separately cultured for 48 h, were used for gene expression analysis by RNA microarray assay."], ["Consent", "n/a"], ["Sample source location", "n/a"]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE59799 not downloaded", "asset:data:geo:GSE59799 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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": ["GSE59799"], "resolved_accessions": ["GSE59799"], "statements": ["The data has been deposited in the Gene Expression Omnibus (GEO) database under the accession number GSE59799."], "basis": "The paper names GSE59799 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484196", "data:geo:GSE59799", "asset:table:pmid:26484196:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59799"]}, "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": "2026-10-31T18:06:03Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 6074, "completion_tokens": 581, "cached_tokens": 2304}}, "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:26484196", "type": "paper", "label": "pmid:26484196"}, {"id": "source:pmid:26484196", "type": "manuscript", "label": "PMID 26484196 full text"}, {"id": "data:geo:GSE59799", "type": "dataset", "label": "GEO GSE59799"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484196", "type": "paper", "label": "pmid:26484196"}, {"id": "source:pmid:26484196", "type": "manuscript", "label": "PMID 26484196 full text"}, {"id": "data:geo:GSE59799", "type": "dataset", "label": "GEO GSE59799"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484196", "type": "extraction", "used": ["source:pmid:26484196"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59799", "type": "accession_resolution", "used": ["data:geo:GSE59799"], "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:26484196", "parent_hash": "sha256:992453a749e50299bd2861e072db2fc53a892d6f6fec10fb31db98acb171af6b", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE59799 licence not read", "asset:data:geo:GSE59799 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ected by the nuclear actin, we have used the microarray analysis to determine the changes in the exp"], "order_basis": "paper_text_order:645", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["changes in the expression levels of RNAs in HeLa cells as a result of EYFP-NLS-actin expressi", "ll culture and RNA isolation HeLa cells were cultured in Dulbecco's modified Eagle's medium (Gibco) s", "s and methods Cell culture and RNA isolation HeLa cells were cultured in Dulbecco's modified E", "% CO2 humidified atmosphere. Transfection of HeLa cells was performed using Lipofectamine 2000"], "order_basis": "paper_text_order:727", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["at 37 °C in a 5% CO2 humidified atmosphere. Transfection of HeLa cells was performed using Lipofectam"], "order_basis": "paper_text_order:1280", "id": "assay:3"}]}