Transcriptomic profiling of human embryonic stem cells upon cell cycle manipulation during pluripotent state dissolution.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697349", "kind": "science-record", "revision": 6, "content_hash": "sha256:8428351d35ef11c76c84eae7e402378dd9d41ed335af0ab0e14a134961b1bf83", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T21:20:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic profiling of human embryonic stem cells upon cell cycle manipulation during pluripotent state dissolution.", "doi": "10.1016/j.gdata.2015.08.032", "pmid": "26697349", "authors": ["Kevin Andrew Uy Gonzales", "Hongqing Liang"], "journal": "Genomics data", "year": 2015, "abstract": "While distinct cell cycle structures have been known to correlate with pluripotent or differentiated cell states [1], there is no evidence on how the cell cycle machinery directly contributes to human embryonic stem cell (hESC) pluripotency. We established a determinant role of cell cycle machineries on the pluripotent state by demonstrating that the specific perturbation of the S and G2 phases can prevent pluripotent state dissolution (PSD) [2]. Active mechanisms in these phases, such as the DNA damage checkpoint and Cyclin B1, promote the pluripotent state [2]. To understand the mechanisms behind the effect on PSD by these pathways in hESCs, we performed comprehensive gene expression analysis by time-course microarray experiments. From these datasets, we observed expression changes in genes involved in the TGFβ signaling pathway, which has a well-established role in hESC maintenance [3], [4], [5]. The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes were obtained using the Significance Analysis of Microarrays software (http://statweb.stanford.edu/~tibs/SAM/) and gene ontology analysis was done using DAVID (https://david.ncifcrf.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697349", "locator": "sections[7] \"Microarray hybridization and analysis\" paragraph 3", "quote": "Differentially expressed genes were obtained using the Significance Analysis of Microarrays software (http://statweb.stanford.edu/~tibs/SAM/) and gene ontology analysis was done using DAVID (https://david.ncifcrf.gov/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697349", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified differentially expressed genes using the Significance Analysis of Microarrays (SAM) software, and deposited the microarray data in NCBI's Gene Expression Omnibus under GEO Series accessions GSE62062 and GSE63215.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697349", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215."}, {"asset": "source:pmid:26697349", "locator": "sections[7] \"Microarray hybridization and analysis\" paragraph 3", "quote": "Differentially expressed genes were obtained using the Significance Analysis of Microarrays software (http://statweb.stanford.edu/~tibs/SAM/) and gene ontology analysis was done using DAVID (https://david.ncifcrf.gov/)."}, {"asset": "source:pmid:26697349", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62062 and http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63215."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified differentially expressed genes using the Significance Analysis of Microarrays (SAM) software, and deposited the microarray data in NCBI's Gene Expression Omnibus under GEO Series accessions GSE62062 and GSE63215.", "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:26697349"], "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:GSE62062"], "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:GSE62062"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697349", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.08.032", "sha256": "sha256:e3fb6609a20228ff6298211f958af7273869ef2a7eed366f7dbe5b11f3b8fe6d", "bytes": 8056, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.08.032", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4664715", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62062", "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=GSE62062", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62062", "version": null, "note": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1519080", "GSM1519081", "GSM1519082", "GSM1519083", "GSM1519084", "GSM1519085", "GSM1519086", "GSM1519087", "GSM1519088", "GSM1519089", "GSM1519090", "GSM1519091", "GSM1519092", "GSM1519093", "GSM1519094", "GSM1519095", "GSM1519096", "GSM1519097", "GSM1519098", "GSM1519099", "GSM1519100", "GSM1519101", "GSM1519102", "GSM1519103", "GSM1519104", "GSM1519105", "GSM1519106", "GSM1519107", "GSM1519108", "GSM1519109", "GSM1519110", "GSM1519111", "GSM1519112", "GSM1519113", "GSM1519114", "GSM1519115", "GSM1519116", "GSM1519117", "GSM1519118", "GSM1519119", "GSM1519120", "GSM1519121", "GSM1519122", "GSM1519123", "GSM1519124", "GSM1519125", "GSM1519126", "GSM1519127"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "An RNAi screen probing signalling control of human embryonic stem cells establishes the cell cycle-regulated restriction of the exit from pluripotency (DNA damage checkpoint)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63215", "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=GSE63215", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63215", "version": null, "note": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1543950", "GSM1543951", "GSM1543952", "GSM1543953", "GSM1543954", "GSM1543955", "GSM1543956", "GSM1543957", "GSM1543958", "GSM1543959", "GSM1543960", "GSM1543961", "GSM1543962", "GSM1543963", "GSM1543964"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "13938", "taxon": "Homo sapiens", "title": "An RNAi screen probing signaling control of human embryonic stem cells establishes the cell cycle-regulated restriction of the exit from pluripotency (CCNB1 overexpression)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE62062 not downloaded", "asset:data:geo:GSE62062 licence not read", "asset:data:geo:GSE63215 not downloaded", "asset:data:geo:GSE63215 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Significance Analysis of Microarrays (SAM)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes were obtained using the Significance Analysis of Microarrays software (http://statweb.stanford.edu/~tibs/SAM/) and gene ontology analysis was done using DAVID (https://david.ncifcrf.gov/)."}}], "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 (Significance Analysis of Microarrays (SAM)), 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": ["GSE62062", "GSE63215"], "resolved_accessions": ["GSE62062", "GSE63215"], "statements": ["The microarray data have been deposited in NCBI's Gene Expression Omnibus (GEO) and can be accessed through GEO Series accession numbers GSE62062 and GSE63215."], "basis": "The paper names GSE62062, GSE63215 in NCBI's 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:26697349", "data:geo:GSE62062"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62062"]}, "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": "2026-10-31T18:26:47Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 20716, "completion_tokens": 4071, "cached_tokens": 2096}}, "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:26697349", "type": "paper", "label": "pmid:26697349"}, {"id": "source:pmid:26697349", "type": "manuscript", "label": "PMID 26697349 full text"}, {"id": "data:geo:GSE62062", "type": "dataset", "label": "GEO GSE62062"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26697349", "type": "paper", "label": "pmid:26697349"}, {"id": "source:pmid:26697349", "type": "manuscript", "label": "PMID 26697349 full text"}, {"id": "data:geo:GSE62062", "type": "dataset", "label": "GEO GSE62062"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26697349", "type": "extraction", "used": ["source:pmid:26697349"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62062", "type": "accession_resolution", "used": ["data:geo:GSE62062"], "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:26697349", "parent_hash": "sha256:995b415b8cc5213e31f6461d9a91915b443ebbbf03d920356b0843e416ecb70f", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE62062 licence not read", "asset:data:geo:GSE62062 not downloaded", "asset:data:geo:GSE63215 licence not read", "asset:data:geo:GSE63215 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.99, "evidence": ["sive gene expression analysis by time-course microarray experiments. From these datasets, we observe", "role in hESC maintenance [3], [4], [5]. The microarray data have been deposited in NCBI's Gene Expr", ". Outline of time-course experiment prior to microarray analysis. Experimental groups and conditions"], "order_basis": "paper_text_order:796", "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": 0.69, "evidence": ["Prior to all treatments, hESCs were instead passaged as single cells using TrypLE™ Express (Life"], "order_basis": "paper_text_order:1587", "id": "assay:2"}]}