← All .science files
pmid:31689238
Molecular basis of senescence transmitting in the population of human endometrial stromal cells.
Anastasiia Griukova · Pavel Deryabin · Alla Shatrova · Elena Burova · Valeria Severino · Annarita Farina · Nikolay Nikolsky · Aleksandra Borodkina
Aging · 2019 doi:10.18632/aging.102441
Paper
complete
Experiment
partial
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 · 8 items
claims array · 2 items
[0] object · 6 fields
evidence array · 2 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 · 1 item
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 · 0 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 5 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
gaps array · 2 items
analysis object · 4 fields
methods array · 4 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
targets array · 0 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 · 1 item
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 · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
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 · 9 items
assays array · 5 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
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[4] 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:31689238", "kind": "science-record", "revision": 7, "content_hash": "sha256:a9f4fbd2ae0a99bd1bde6358fd63b9f25e7576553c7d8c3a755808271700bdb8", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Molecular basis of senescence transmitting in the population of human endometrial stromal cells.", "doi": "10.18632/aging.102441", "pmid": "31689238", "authors": ["Anastasiia Griukova", "Pavel Deryabin", "Alla Shatrova", "Elena Burova", "Valeria Severino", "Annarita Farina", "Nikolay Nikolsky", "Aleksandra Borodkina"], "journal": "Aging", "year": 2019, "abstract": "Hormone-regulated proliferation and differentiation of endometrial stromal cells (ESCs) determine overall endometrial plasticity and receptivity to embryos. Previously we revealed that ESCs may undergo premature senescence, accompanied by proliferation loss and various intracellular alterations. Here we focused on whether and how senescence may be transmitted within the ESCs population. We revealed that senescent ESCs may induce paracrine senescence in young counterparts via cell contacts, secreted factors and extracellular vesicles. According to secretome-wide profiling we identified plasminogen activator inhibitor -1 (PAI-1) to be the most prominent protein secreted by senescent ESCs (data are available via ProteomeXchange with identifier PXD015742). By applying CRISPR/Cas9 techniques we disclosed that PAI-1 secreted by senescent ESCs may serve as the master-regulator of paracrine senescence progression within the ESCs population. Unraveled molecular basis of senescence transduction in the ESCs population may be further considered in terms of altered endometrial plasticity and sensitivity to invading embryo, thus contributing to the female infertility curing.", "claims": [{"id": "claim-method", "statement": "The statistical evaluation of proteins differentially expressed between the CM-ctr and CM-sen samples was performed by applying the T-test with Hochberg-Benjamini correction (p<0.05). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [52] partner repository with the dataset identifier PXD015742 and 10.6019/PXD015742.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31689238", "locator": "sections[22] \"Quantitative analysis and bioinformatics\" paragraph 2", "quote": "The statistical evaluation of proteins differentially expressed between the CM-ctr and CM-sen samples was performed by applying the T-test with Hochberg-Benjamini correction (p<0.05)."}, {"asset": "source:pmid:31689238", "locator": "sections[21] \"LC-MS/MS configuration and protein identification\" paragraph 4", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [52] partner repository with the dataset identifier PXD015742 and 10.6019/PXD015742."}], "state": "complete"}, {"id": "claim-data-access", "statement": "(data are available via ProteomeXchange with identifier PXD015742)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31689238", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "(data are available via ProteomeXchange with identifier PXD015742)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:31689238"], "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:PXD015742"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "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:PXD015742"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31689238", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.102441", "sha256": "sha256:a67bb1ab53f13fb611d82bcd61863eaaefc615cb536e64cda25410e6c1bf0ba2", "bytes": 54630, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.102441", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6874437", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD015742", "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=PXD015742", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD015742", "version": null, "note": "(data are available via ProteomeXchange with identifier PXD015742)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "(data are available via ProteomeXchange with identifier PXD015742)", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Molecular basis of senescence transmitting in the population of human endometrial stromal cells", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31689238:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bc83e1b5db381473e10fd88324b850219621062d20a928035a8502455150a930", "bytes": 440, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#t1", "version": null, "note": "Primer oligonucleotide sequences.", "structure": {"pmcid": "PMC6874437", "section_index": 24, "section_title": "RNA extraction, reverse transcription and real time PCR", "row_count": 5, "column_count": 3}, "table": {"label": "Table 1", "caption": "Primer oligonucleotide sequences.", "rows": [["N", "Oligonucleotide", "Sequence"], ["1", "PAI-1 forward", "5′-CAGAAACAGTGTGCATGGGTTA-3′"], ["2", "PAI-1 reverse", "5′-CACGCATCTGACATTTCTTCCT-3′"], ["3", "GAPDH forward", "5′-GAGGTCAATGAAGGGGTCAT-3′"], ["4", "GAPDH reverse", "5′-AGTCAACGGATTTGGTCGTA-3′"]], "row_count": 5, "column_count": 3, "numeric_cells": 10, "header_rows": 0, "locator": "section[24]/table-wrap[1]#t1"}}], "gaps": ["asset:data:geo:PXD015742 not downloaded", "asset:data:geo:PXD015742 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-4", "family": null, "specific": null, "label": "T-test with Hochberg-Benjamini correction (p<0.05)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "The statistical evaluation of proteins differentially expressed between the CM-ctr and CM-sen samples was performed by applying the T-test with Hochberg-Benjamini correction (p<0.05). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [52] partner repository with the dataset identifier PXD015742 and 10.6019/PXD015742."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_mann_whitney"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "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": ["PXD015742"], "resolved_accessions": ["PXD015742"], "statements": ["(data are available via ProteomeXchange with identifier PXD015742)"], "basis": "The paper names PXD015742 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31689238", "data:geo:PXD015742", "asset:table:pmid:31689238:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD015742"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:40Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39349, "completion_tokens": 1525, "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:31689238", "type": "paper", "label": "pmid:31689238"}, {"id": "source:pmid:31689238", "type": "manuscript", "label": "PMID 31689238 full text"}, {"id": "data:geo:PXD015742", "type": "dataset", "label": "GEO PXD015742"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31689238", "type": "paper", "label": "pmid:31689238"}, {"id": "source:pmid:31689238", "type": "manuscript", "label": "PMID 31689238 full text"}, {"id": "data:geo:PXD015742", "type": "dataset", "label": "GEO PXD015742"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31689238", "type": "extraction", "used": ["source:pmid:31689238"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD015742", "type": "accession_resolution", "used": ["data:geo:PXD015742"], "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:31689238", "parent_hash": "sha256:a782e15ecd3f8d3c11956723a4b5df9ba9550db890903c53009ee5f45c6a9144", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD015742 licence not read", "asset:data:geo:PXD015742 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "assays": [{"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": ["ange with identifier PXD015742). By applying CRISPR/Cas9 techniques we disclosed that PAI-1 secr"], "order_basis": "paper_text_order:827", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e identified by liquid chromatography tandem-mass spectrometry (LC-MS/MS) and the following bioinformatic a", "uid chromatography tandem-mass spectrometry (LC-MS/MS) and the following bioinformatic analysis. G", "ion of all peptides identified within CMs by LC-MS/MS. (B) Volcano plot of proteins differentially", "ive secretome analysis by applying a shotgun proteomic strategy. Proteins from CM obtained from you"], "order_basis": "paper_text_order:1277", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["of cell migration and positive regulation of apoptosis. Interestingly, among down-regulated protein"], "order_basis": "paper_text_order:3575", "id": "assay:3"}, {"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": ["l blood from healthy donor (line 2804), were cultured in DMEM/F12 (Gibco BRL, USA) supplemented with", "nsity of 7.5*103 cells per cm2. HEK293T were cultured in DMEM (Biolot, Russian Federation) The study"], "order_basis": "paper_text_order:4729", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Mann-Whitney"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}