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pmid:29069483
Protein profile of mouse ovarian follicles grown in vitro.
Amandine Anastácio · Kenny A Rodriguez-Wallberg · Solenne Chardonnet · Cédric Pionneau · Christian Fédérici · Teresa Almeida Santos · Catherine Poirot
Molecular human reproduction · 2017 doi:10.1093/molehr/gax056
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29069483", "kind": "science-record", "revision": 8, "content_hash": "sha256:d8d37d96233e3cbb30b9418be656b95ac10de18102a0dd4875bc42f3c2e28788", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T22:43:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Protein profile of mouse ovarian follicles grown in vitro.", "doi": "10.1093/molehr/gax056", "pmid": "29069483", "authors": ["Amandine Anastácio", "Kenny A Rodriguez-Wallberg", "Solenne Chardonnet", "Cédric Pionneau", "Christian Fédérici", "Teresa Almeida Santos", "Catherine Poirot"], "journal": "Molecular human reproduction", "year": 2017, "abstract": "STUDY QUESTION: Could the follicle proteome be mapped by identifying specific proteins that are common or differ between three developmental stages from the secondary follicle (SF) to the antrum-like stage?\nSUMMARY ANSWER: From a total of 1401 proteins identified in the follicles, 609 were common to the three developmental stages investigated and 444 were found uniquely at one of the stages.\nWHAT IS KNOWN ALREADY: The importance of the follicle as a functional structure has been recognized; however, up-to-date the proteome of the whole follicle has not been described. A few studies using proteomics have previously reported on either isolated fully-grown oocytes before or after meiosis resumption or cumulus cells.\nSTUDY DESIGN, SIZE, DURATION: The experimental design included a validated mice model for isolation and individual culture of SFs. The system was chosen as it allows continuous evaluation of follicle growth and selection of follicles for analysis at pre-determined developmental stages: SF, complete Slavjanski membrane rupture (SMR) and antrum-like cavity (AF). The experiments were repeated 13 times independently to acquire the material that was analyzed by proteomics.\nPARTICIPANTS/MATERIALS, SETTING, METHODS: SFs (n = 2166) were isolated from B6CBA/F1 female mice (n = 42), 12 days old, from 15 l. About half of the follicles isolated as SF were analyzed as such (n = 1143) and pooled to obtain 139 μg of extracted protein. Both SMR (n = 359) and AF (n = 124) were obtained after individual culture of 1023 follicles in a microdrop system under oil, selected for analysis and pooled, to obtain 339 μg and 170 μg of protein, respectively. The follicle proteome was analyzed combining isoelectric focusing (IEF) fractionation with 1D and 2D LC-MS/MS analysis to enhance protein identification. The three protein lists were submitted to the 'Compare gene list' tool in the PANTHER website to gain insights on the Gene Ontology Biological processes present and to Ingenuity Pathway Analysis to highlight protein networks. A label-free quantification was performed with 1D LC-MS/MS analyses to emphasize proteins with different expression profiles between the three follicular stages. Supplementary western blot analysis (using new biological replicates) was performed to confirm the expression variations of three proteins during follicle development in vitro.\nMAIN RESULTS AND THE ROLE OF CHANCE: It was found that 609 out of 1401 identified proteins were common to the three follicle developmental stages investigated. Some proteins were identified uniquely at one stage: 71 of the 775 identified proteins in SF, 181 of 1092 in SMR and 192 of 1100 in AF. Additional qualitative and quantitative analysis highlighted 44 biological processes over-represented in our samples compared to the Mus musculus gene database. In particular, it was possible to identify proteins implicated in the cell cycle, calcium ion binding and glycolysis, with specific expressions and abundance, throughout in vitro follicle development.\nLARGE SCALE DATA: Data are available via ProteomeXchange with identifier PXD006227.\nLIMITATIONS, REASONS FOR CAUTION: The proteome analyses described in this study were performed after in vitro development. Despite fractionation of the samples before LC-MS/MS, proteomic approaches are not exhaustive, thus proteins that are not identified in a group are not necessarily absent from that group, although they are likely to be less abundant.\nWIDER IMPLICATIONS OF THE FINDINGS: This study allowed a general view of proteins implicated in follicle development in vitro and it represents the most complete catalog of the whole follicle proteome available so far. Not only were well known proteins of the oocyte identified but also proteins that are probably expressed only in granulosa cells.\nSTUDY FUNDING/COMPETING INTEREST(S): This study was supported by the Portuguese Foundation for Science and Technology, FCT (PhD fellowship SFRH/BD/65299/2009 to A.A.), the Swedish Childhood Cancer Foundation (PR 2014-0144 to K.A.R-.W.) and Stockholm County Council to K.A.R-.W. The authors of the study have no conflict of interest to report.", "claims": [{"id": "claim-method", "statement": "Only proteins with a fold-change >2 between the groups (ANOVA P-value < 0.05), and with at least two peptides with significant changes (ANOVA q-value < 0.05 and fold-change >2), were accepted.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29069483", "locator": "sections[13] \"Label-free quantification\" paragraph 3", "quote": "Only proteins with a fold-change >2 between the groups (ANOVA P-value < 0.05), and with at least two peptides with significant changes (ANOVA q-value < 0.05 and fold-change >2), were accepted."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD006227.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29069483", "locator": "sections[0] \"Abstract\" paragraph 7", "quote": "Data are available via ProteomeXchange with identifier PXD006227."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used label-free quantification with 1D LC-MS/MS to assess stage-specific protein abundance, and the source data are available through ProteomeXchange under identifier PXD006227.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29069483", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "A label-free quantification was performed with 1D LC-MS/MS analyses to emphasize proteins with different expression profiles between the three follicular stages."}, {"asset": "source:pmid:29069483", "locator": "sections[0] \"Abstract\" paragraph 7", "quote": "Data are available via ProteomeXchange with identifier PXD006227."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used label-free quantification with 1D LC-MS/MS to assess stage-specific protein abundance, and the source data are available through ProteomeXchange under identifier PXD006227.", "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:29069483"], "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. 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"access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD006227.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Protein profile of mouse ovarian follicles grown in vitro", "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:29069483:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9ea741d8db6f6bd85afce27d606bec4a23cfc054a01850794c34ee66ba4c6de", "bytes": 5594, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#gax056TB1", "version": null, "note": "Proteins differently expressed in the three stages.", "structure": {"pmcid": "PMC5909860", "section_index": 20, "section_title": "Analysis of protein-abundance in the three developmental stages", "row_count": 58, "column_count": 9}, "table": {"label": "Table I", "caption": "Proteins differently expressed in the three stages.", "rows": [["Accession number", "Protein name", "Gene name", "Protein score", "ANOVA P-value", "Fold-change", "Max.", "Min.", "Profile Type (Fig. 7)"], ["Q8K3V4", "Protein-arginine deiminase type-6", "Padi6", "1103.2", "1.9E-07", "3.6", "SF", "AF", "P1"], ["P16125", "L-lactate dehydrogenase B chain", "Ldhb", "879.7", "7.0E-06", "4.9", "SF", "AF", "P1"], ["F8WIV2", "Protein Serpinb6a", "Serpinb6a", "648.1", "3.4E-07", "2.4", "SF", "AF", "P1"], ["Q9CWU5", "KH domain-containing protein 3", "Khdc3", "569.8", "5.9E-05", "3.2", "SF", "SMR/AF", "P1"], ["Q9R0P9", "Ubiquitin carboxyl-terminal hydrolase isozyme L1", "Uchl1", "509.7", "6.9E-05", "4.4", "SF", "AF", "P1"], ["P24549", "Retinal dehydrogenase 1", "Aldh1a1", "418.6", "8.0E-04", "2.0", "SF", "SMR", "P1"], ["P10761", "Zona pellucida sperm-binding protein 3", "Zp3", "346.3", "7.2E-05", "4.9", "SF", "AF", "P1"], ["P54869", "Hydroxymethylglutaryl-CoA synthase, mitochondrial", "Hmgcs2", "335.2", "1.0E-02", "2.1", "SF", "SMR", "P1"], ["Q9DAW9", "Calponin-3", "Cnn3", "308.2", "2.3E-04", "2.5", "SF", "AF", "P1"], ["Q9WVB3", "Transducin-like enhancer protein 6", "Tle6", "239.0", "1.9E-06", "3.5", "SF", "AF", "P1"], ["P10518", "Delta-aminolevulinic acid dehydratase", "Alad", "230.6", "2.0E-04", "2.7", "SF", "AF", "P1"], ["P20239", "Zona pellucida sperm-binding protein 2", "Zp2", "189.8", "7.0E-05", "2.6", "SF", "AF", "P1"], ["Q08EC7", "Pla2g4c protein", "Pla2g4c", "188.0", "2.4E-04", "3.1", "SF", "AF", "P1"], ["P24472", "Glutathione S-transferase A4", "Gsta4", "153.6", "3.3E-04", "2.7", "SF", "SMR", "P1"], ["Q9CWE6", "Oocyte-expressed protein homolog", "Ooep", "94.9", "2.0E-02", "4.8", "SF", "SMR/AF", "P1"], ["P14211", "Calreticulin", "Calr", "276.5", "1.3E-05", "4.6", "SMR", "SF", "P2"], ["Q60817", "Nascent polypeptide-associated complex subunit alpha", "Naca", "270.9", "1.6E-04", "2.3", "SMR", "AF", "P2"], ["Q60605", "Myosin light polypeptide 6", "Myl6", "174.3", "1.6E-03", "3.4", "SMR", "SF/AF", "P2"], ["G3UWR0", "Calumenin", "Calu", "161.2", "5.1E-05", "3.1", "SMR", "SF", "P2"], ["Q4VAA2", "Protein CDV3", "Cdv3", "106.5", "2.1E-04", "2.5", "SMR", "AF", "P2"], ["P20029", "78 kDa glucose-regulated protein", "Hspa5", "2951.4", "2.6E-05", "2.7", "AF", "SF", "P3"], ["P17182", "Alpha-enolase", "Eno1", "1548.7", "4.5E-07", "5.0", "AF", "SF", "P3"], ["P05213", "Tubulin alpha-1B chain", "Tuba1b", "1527.4", "7.0E-04", "2.7", "AF", "SF", "P3"], ["P09103", "Protein disulfide-isomerase", "P4hb", "1416.4", "4.3E-06", "2.7", "AF", "SF", "P3"], ["P16858", "Glyceraldehyde-3-phosphate dehydrogenase", "Gapdh", "701.4", "1.6E-07", "4.0", "AF", "SF", "P3"], ["P14152", "Malate dehydrogenase, cytoplasmic", "Mdh1", "462.0", "4.8E-06", "2.1", "AF", "SF", "P3"], ["P48036", "Annexin A5", "Anxa5", "445.8", "5.5E-04", "2.0", "AF", "SF", "P3"], ["Q99KV1", "DnaJ homolog subfamily B member 11", "Dnajb11", "420.4", "1.1E-03", "2.2", "AF", "SF", "P3"], ["G5E8N5", "L-lactate dehydrogenase", "Ldha", "412.5", "3.1E-06", "3.4", "AF", "SF", "P3"], ["P24815", "3 beta-hydroxysteroid dehydrogenase/Delta 5-- > 4-isomerase type 1", "Hsd3b1", "394.6", "6.4E-03", "3.1", "AF", "SF", "P3"], ["E9PXX7", "Thioredoxin domain-containing protein 5", "Txndc5", "380.2", "4.7E-03", "2.1", "AF", "SF", "P3"], ["P57759", "Endoplasmic reticulum resident protein 29", "Erp29", "361.6", "3.1E-05", "2.5", "AF", "SF", "P3"], ["O08807", "Peroxiredoxin-4", "Prdx4", "358.2", "4.0E-05", "2.2", "AF", "SF", "P3"], ["P29758", "Ornithine aminotransferase, mitochondrial", "Oat", "354.1", "5.3E-04", "2.1", "AF", "SF", "P3"], ["P51656", "Estradiol 17-beta-dehydrogenase 1", "Hsd17b1", "351.2", "3.6E-03", "2.4", "AF", "SF", "P3"], ["P53994", "Ras-related protein Rab-2A", "Rab2a", "330.6", "3.3E-03", "2.0", "AF", "SF", "P3"], ["Q9DBJ1", "Phosphoglycerate mutase 1", "Pgam1", "329.4", "6.5E-04", "2.2", "AF", "SF", "P3"], ["P17742", "Peptidyl-prolyl cis-trans isomerase A", "Ppia", "325.5", "5.8E-03", "2.2", "SMR", "SF", "P3"], ["P09411", "Phosphoglycerate kinase 1", "Pgk1", "300.5", "2.8E-03", "2.7", "AF", "SF", "P3"], ["Q60715", "Prolyl 4-hydroxylase subunit alpha-1", "P4ha1", "271.1", "7.0E-05", "2.2", "AF", "SF", "P3"], ["Q9QXT0", "Protein canopy homolog 2", "Cnpy2", "254.6", "3.8E-03", "2.3", "SMR", "SF", "P3"], ["A2A7Q5", "Prolyl 3-hydroxylase 1", "Lepre1", "225.9", "2.7E-03", "2.3", "AF", "SF", "P3"], ["G5E850", "Cytochrome b-5, isoform CRA_a", "Cyb5", "222.6", "4.9E-05", "3.4", "AF", "SF", "P3"], ["Q3U4W8", "Ubiquitin carboxyl-terminal hydrolase", "Usp5", "216.6", "5.5E-03", "2.2", "AF", "SF", "P3"], ["G3XA14", "Protein Akr1cl", "Akr1cl", "212.7", "7.5E-03", "3.4", "SMR", "SF", "P3"], ["P34884", "Macrophage migration inhibitory factor", "Mif", "210.1", "1.6E-05", "2.1", "AF", "SF", "P3"], ["P22935", "Cellular retinoic acid-binding protein 2", "Crabp2", "130.9", "2.2E-04", "2.6", "AF", "SF", "P3"], ["Q9CYA0", "Cysteine-rich with EGF-like domain protein 2", "Creld2", "107.5", "2.0E-02", "2.9", "AF", "SF", "P3"], ["P63158", "High-mobility group protein B1", "Hmgb1", "267.9", "2.0E-03", "2.5", "SF", "SMR", "P4"], ["Q9JKB1", "Ubiquitin carboxyl-terminal hydrolase isozyme L3", "Uchl3", "226.8", "1.1E-03", "2.6", "SF", "SMR", "P4"], ["Q9ERD7", "Tubulin beta-3 chain", "Tubb3", "1342.8", "1.6E-03", "3.3", "AF", "SMR", "P5"], ["P31324", "cAMP-dependent protein kinase type II-beta regulatory subunit", "Prkar2b", "1129.2", "1.7E-04", "3.7", "AF", "SF", "P5"], ["Q05816", "Fatty acid-binding protein, epidermal", "Fabp5", "781.9", "9.1E-05", "3.1", "AF", "SF", "P5"], ["P17751", "Triosephosphate isomerase", "Tpi1", "627.6", "5.7E-05", "2.3", "AF", "SF", "P5"], ["Q9D0F9", "Phosphoglucomutase-1", "Pgm1", "403.2", "1.2E-04", "2.3", "AF", "SF/SMR", "P5"], ["Q99JF5", "Diphosphomevalonate decarboxylase", "Mvd", "161.0", "9.7E-05", "3.6", "AF", "SF", "P5"], ["Q62159", "Rho-related GTP-binding protein RhoC", "Rhoc", "136.3", "2.1E-04", "2.4", "AF", "SMR", "P5"]], "row_count": 58, "column_count": 9, "numeric_cells": 241, "header_rows": 1, "locator": "section[20]/table-wrap[1]#gax056TB1"}}, {"id": "asset:table:pmid:29069483:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9ea741d8db6f6bd85afce27d606bec4a23cfc054a01850794c34ee66ba4c6de", "bytes": 5594, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#gax056TB1", "version": null, "note": "Proteins differently expressed in the three stages.", "structure": {"pmcid": "PMC5909860", "section_index": 23, "section_title": "Analysis of protein-abundance in the three developmental stages", "row_count": 58, "column_count": 9}, "table": {"label": "Table I", "caption": "Proteins differently expressed in the three stages.", "rows": [["Accession number", "Protein name", "Gene name", "Protein score", "ANOVA P-value", "Fold-change", "Max.", "Min.", "Profile Type (Fig. 7)"], ["Q8K3V4", "Protein-arginine deiminase type-6", "Padi6", "1103.2", "1.9E-07", "3.6", "SF", "AF", "P1"], ["P16125", "L-lactate dehydrogenase B chain", "Ldhb", "879.7", "7.0E-06", "4.9", "SF", "AF", "P1"], ["F8WIV2", "Protein Serpinb6a", "Serpinb6a", "648.1", "3.4E-07", "2.4", "SF", "AF", "P1"], ["Q9CWU5", "KH domain-containing protein 3", "Khdc3", "569.8", "5.9E-05", "3.2", "SF", "SMR/AF", "P1"], ["Q9R0P9", "Ubiquitin carboxyl-terminal hydrolase isozyme L1", "Uchl1", "509.7", "6.9E-05", "4.4", "SF", "AF", "P1"], ["P24549", "Retinal dehydrogenase 1", "Aldh1a1", "418.6", "8.0E-04", "2.0", "SF", "SMR", "P1"], ["P10761", "Zona pellucida sperm-binding protein 3", "Zp3", "346.3", "7.2E-05", "4.9", "SF", "AF", "P1"], ["P54869", "Hydroxymethylglutaryl-CoA synthase, mitochondrial", "Hmgcs2", "335.2", "1.0E-02", "2.1", "SF", "SMR", "P1"], ["Q9DAW9", "Calponin-3", "Cnn3", "308.2", "2.3E-04", "2.5", "SF", "AF", "P1"], ["Q9WVB3", "Transducin-like enhancer protein 6", "Tle6", "239.0", "1.9E-06", "3.5", "SF", "AF", "P1"], ["P10518", "Delta-aminolevulinic acid dehydratase", "Alad", "230.6", "2.0E-04", "2.7", "SF", "AF", "P1"], ["P20239", "Zona pellucida sperm-binding protein 2", "Zp2", "189.8", "7.0E-05", "2.6", "SF", "AF", "P1"], ["Q08EC7", "Pla2g4c protein", "Pla2g4c", "188.0", "2.4E-04", "3.1", "SF", "AF", "P1"], ["P24472", "Glutathione S-transferase A4", "Gsta4", "153.6", "3.3E-04", "2.7", "SF", "SMR", "P1"], ["Q9CWE6", "Oocyte-expressed protein homolog", "Ooep", "94.9", "2.0E-02", "4.8", "SF", "SMR/AF", "P1"], ["P14211", "Calreticulin", "Calr", "276.5", "1.3E-05", "4.6", "SMR", "SF", "P2"], ["Q60817", "Nascent polypeptide-associated complex subunit alpha", "Naca", "270.9", "1.6E-04", "2.3", "SMR", "AF", "P2"], ["Q60605", "Myosin light polypeptide 6", "Myl6", "174.3", "1.6E-03", "3.4", "SMR", "SF/AF", "P2"], ["G3UWR0", "Calumenin", "Calu", "161.2", "5.1E-05", "3.1", "SMR", "SF", "P2"], ["Q4VAA2", "Protein CDV3", "Cdv3", "106.5", "2.1E-04", "2.5", "SMR", "AF", "P2"], ["P20029", "78 kDa glucose-regulated protein", "Hspa5", "2951.4", "2.6E-05", "2.7", "AF", "SF", "P3"], ["P17182", "Alpha-enolase", "Eno1", "1548.7", "4.5E-07", "5.0", "AF", "SF", "P3"], ["P05213", "Tubulin alpha-1B chain", "Tuba1b", "1527.4", "7.0E-04", "2.7", "AF", "SF", "P3"], ["P09103", "Protein disulfide-isomerase", "P4hb", "1416.4", "4.3E-06", "2.7", "AF", "SF", "P3"], ["P16858", "Glyceraldehyde-3-phosphate dehydrogenase", "Gapdh", "701.4", "1.6E-07", "4.0", "AF", "SF", "P3"], ["P14152", "Malate dehydrogenase, cytoplasmic", "Mdh1", "462.0", "4.8E-06", "2.1", "AF", "SF", "P3"], ["P48036", "Annexin A5", "Anxa5", "445.8", "5.5E-04", "2.0", "AF", "SF", "P3"], ["Q99KV1", "DnaJ homolog subfamily B member 11", "Dnajb11", "420.4", "1.1E-03", "2.2", "AF", "SF", "P3"], ["G5E8N5", "L-lactate dehydrogenase", "Ldha", "412.5", "3.1E-06", "3.4", "AF", "SF", "P3"], ["P24815", "3 beta-hydroxysteroid dehydrogenase/Delta 5-- > 4-isomerase type 1", "Hsd3b1", "394.6", "6.4E-03", "3.1", "AF", "SF", "P3"], ["E9PXX7", "Thioredoxin domain-containing protein 5", "Txndc5", "380.2", "4.7E-03", "2.1", "AF", "SF", "P3"], ["P57759", "Endoplasmic reticulum resident protein 29", "Erp29", "361.6", "3.1E-05", "2.5", "AF", "SF", "P3"], ["O08807", "Peroxiredoxin-4", "Prdx4", "358.2", "4.0E-05", "2.2", "AF", "SF", "P3"], ["P29758", "Ornithine aminotransferase, mitochondrial", "Oat", "354.1", "5.3E-04", "2.1", "AF", "SF", "P3"], ["P51656", "Estradiol 17-beta-dehydrogenase 1", "Hsd17b1", "351.2", "3.6E-03", "2.4", "AF", "SF", "P3"], ["P53994", "Ras-related protein Rab-2A", "Rab2a", "330.6", "3.3E-03", "2.0", "AF", "SF", "P3"], ["Q9DBJ1", "Phosphoglycerate mutase 1", "Pgam1", "329.4", "6.5E-04", "2.2", "AF", "SF", "P3"], ["P17742", "Peptidyl-prolyl cis-trans isomerase A", "Ppia", "325.5", "5.8E-03", "2.2", "SMR", "SF", "P3"], ["P09411", "Phosphoglycerate kinase 1", "Pgk1", "300.5", "2.8E-03", "2.7", "AF", "SF", "P3"], ["Q60715", "Prolyl 4-hydroxylase subunit alpha-1", "P4ha1", "271.1", "7.0E-05", "2.2", "AF", "SF", "P3"], ["Q9QXT0", "Protein canopy homolog 2", "Cnpy2", "254.6", "3.8E-03", "2.3", "SMR", "SF", "P3"], ["A2A7Q5", "Prolyl 3-hydroxylase 1", "Lepre1", "225.9", "2.7E-03", "2.3", "AF", "SF", "P3"], ["G5E850", "Cytochrome b-5, isoform CRA_a", "Cyb5", "222.6", "4.9E-05", "3.4", "AF", "SF", "P3"], ["Q3U4W8", "Ubiquitin carboxyl-terminal hydrolase", "Usp5", "216.6", "5.5E-03", "2.2", "AF", "SF", "P3"], ["G3XA14", "Protein Akr1cl", "Akr1cl", "212.7", "7.5E-03", "3.4", "SMR", "SF", "P3"], ["P34884", "Macrophage migration inhibitory factor", "Mif", "210.1", "1.6E-05", "2.1", "AF", "SF", "P3"], ["P22935", "Cellular retinoic acid-binding protein 2", "Crabp2", "130.9", "2.2E-04", "2.6", "AF", "SF", "P3"], ["Q9CYA0", "Cysteine-rich with EGF-like domain protein 2", "Creld2", "107.5", "2.0E-02", "2.9", "AF", "SF", "P3"], ["P63158", "High-mobility group protein B1", "Hmgb1", "267.9", "2.0E-03", "2.5", "SF", "SMR", "P4"], ["Q9JKB1", "Ubiquitin carboxyl-terminal hydrolase isozyme L3", "Uchl3", "226.8", "1.1E-03", "2.6", "SF", "SMR", "P4"], ["Q9ERD7", "Tubulin beta-3 chain", "Tubb3", "1342.8", "1.6E-03", "3.3", "AF", "SMR", "P5"], ["P31324", "cAMP-dependent protein kinase type II-beta regulatory subunit", "Prkar2b", "1129.2", "1.7E-04", "3.7", "AF", "SF", "P5"], ["Q05816", "Fatty acid-binding protein, epidermal", "Fabp5", "781.9", "9.1E-05", "3.1", "AF", "SF", "P5"], ["P17751", "Triosephosphate isomerase", "Tpi1", "627.6", "5.7E-05", "2.3", "AF", "SF", "P5"], ["Q9D0F9", "Phosphoglucomutase-1", "Pgm1", "403.2", "1.2E-04", "2.3", "AF", "SF/SMR", "P5"], ["Q99JF5", "Diphosphomevalonate decarboxylase", "Mvd", "161.0", "9.7E-05", "3.6", "AF", "SF", "P5"], ["Q62159", "Rho-related GTP-binding protein RhoC", "Rhoc", "136.3", "2.1E-04", "2.4", "AF", "SMR", "P5"]], "row_count": 58, "column_count": 9, "numeric_cells": 241, "header_rows": 1, "locator": "section[20]/table-wrap[1]#gax056TB1"}}], "gaps": ["asset:data:geo:PXD006227 not downloaded", "asset:data:geo:PXD006227 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Only proteins with a fold-change >2 between the groups (ANOVA P-value < 0.05), and with at least two peptides with significant changes (ANOVA q-value < 0.05 and fold-change >2), were accepted."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": 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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": ["PXD006227"], "resolved_accessions": ["PXD006227"], "statements": ["Data are available via ProteomeXchange with identifier PXD006227."], "basis": "The paper names PXD006227 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:29069483", "data:geo:PXD006227", "asset:table:pmid:29069483:1", "asset:table:pmid:29069483:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006227"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:40Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 113148, "completion_tokens": 2966, "cached_tokens": 29208}}, "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:29069483", "type": "paper", "label": "pmid:29069483"}, {"id": "source:pmid:29069483", "type": "manuscript", "label": "PMID 29069483 full text"}, {"id": "data:geo:PXD006227", "type": "dataset", "label": "GEO PXD006227"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29069483", "type": "paper", "label": "pmid:29069483"}, {"id": "source:pmid:29069483", "type": "manuscript", "label": "PMID 29069483 full text"}, {"id": "data:geo:PXD006227", "type": "dataset", "label": "GEO PXD006227"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29069483", "type": "extraction", "used": ["source:pmid:29069483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006227", "type": "accession_resolution", "used": ["data:geo:PXD006227"], "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:29069483", "parent_hash": "sha256:ebfaf49b90de57f161d879027feffbd7b53b703ac6bffe64390969d84a5eaef9", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD006227 licence not read", "asset:data:geo:PXD006227 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Protein profile of mouse ovarian follicles grown in vitro.", "cretion, and it is the main source of ATP in mouse preantral follicles in vitro (Boland et al.,"], "order_basis": "paper_text_order:0", "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": ["focusing (IEF) fractionation with 1D and 2D LC-MS/MS analysis to enhance protein identification.", "el-free quantification was performed with 1D LC-MS/MS analyses to emphasize proteins with differen", "Despite fractionation of the samples before LC-MS/MS, proteomic approaches are not exhaustive, th", "to acquire the material that was analyzed by proteomics. PARTICIPANTS/MATERIALS, SETTING, METHODS: S"], "order_basis": "paper_text_order:1198", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["n the three follicular stages. Supplementary western blot analysis (using new biological replicates) w", "Protein-abundance results were validated by western blot analysis of selected proteins, namely PKAR2B", "d proteins, namely PKAR2B and LDHB (Fig. 9). Western blot demonstrating variable expression of PRKAR2B", "during follicle development is also shown by western blot, with similar abundance in the SMR and AF st"], "order_basis": "paper_text_order:2237", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Only proteins with a fold-change >2 between the groups (ANOVA P-value < 0.05), and with at least two peptides with significant changes (ANOVA q-value < 0.05 and fold-change >2), were accepted."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}