Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25478318", "kind": "science-record", "revision": 6, "content_hash": "sha256:12f3556dc4f8ff5533022fb19896f52cdc4195590805ca9f45efc0bdf1dd7c64", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T21:19:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis.", "doi": "10.1016/j.gdata.2014.10.015", "pmid": "25478318", "authors": ["Abby L Manthey", "Anne M Terrell", "Salil A Lachke", "Shawn W Polson", "Melinda K Duncan"], "journal": "Genomics data", "year": 2014, "abstract": "Next-generation sequencing of the transcriptome (RNA-Seq) is a powerful method that allows for the quantitative determination of absolute gene expression, and can be used to investigate how these levels change in response to an experimental manipulation or disease condition. The sensitivity of this method allows one to analyze transcript levels of all expressed genes, including low abundance transcripts that encode important regulatory molecules, providing valuable insights into the global effects of experimental manipulations. However, this increased sensitivity can also make it challenging to ascertain which expression changes are biologically significant. Here, we describe a novel set of filtering criteria - based on biological insights and computational approaches - that were applied to prioritize genes for further study from an extensive number of differentially expressed transcripts in lenses lacking Smad interacting protein 1 (Sip1) obtained via RNA-Seq by Manthey and colleagues in Mechanisms of Development (Manthey et al., 2014). Notably, this workflow allowed an original list of over 7,100 statistically significant differentially expressed genes (DEGs) to be winnowed down to 190 DEGs that likely play a biologically significant role in Sip1 function during lens development. Focusing on genes whose expression was upregulated or downregulated in a manner opposite to what normally occurs during lens development, we identified 78 genes that appear to be strongly dependent on Sip1 function. From these data (GEO accession number GSE49949), it appears that Sip1 regulates multiple genes in the lens that are generally distinct from those regulated by Sip1 in other cellular contexts, including genes whose expression is prominent in the early head ectoderm, from which the lens differentiates. Further, the analysis criteria outlined here represent a filtering scheme that can be used to prioritize genes in future RNA-Seq investigations performed at this stage of ocular lens development.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were identified by calculating the variance from a beta binomial distribution using the method of Baggerly et al. [8] against quantile normalized observed counts [reviewed in [9]] producing per gene p-values that were false discovery rate (FDR) corrected for multiple comparison [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25478318", "locator": "sections[7] \"Gene mapping and normalization\" paragraph 3", "quote": "Differentially expressed genes (DEGs) were identified by calculating the variance from a beta binomial distribution using the method of Baggerly et al. [8] against quantile normalized observed counts [reviewed in [9]] producing per gene p-values that were false discovery rate (FDR) corrected for multiple comparison [10]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49949.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25478318", "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=GSE49949."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A filtering workflow reduced 7,108 statistically significant differentially expressed genes to 190 biologically relevant genes, of which 78 appeared strongly dependent on Sip1 function; differential expression was assessed using a beta-binomial variance model, and the source RNA-Seq data are available through GEO accession GSE49949.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25478318", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Notably, this workflow allowed an original list of over 7100 statistically significant differentially expressed genes (DEGs) to be winnowed down to 190 DEGs that likely play a biologically significant role in Sip1 function during lens development."}, {"asset": "source:pmid:25478318", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Focusing on genes whose expression was upregulated or downregulated in a manner opposite to what normally occurs during lens development, we identified 78 genes that appear to be strongly dependent on Sip1 function."}, {"asset": "source:pmid:25478318", "locator": "sections[7] \"Gene mapping and normalization\" paragraph 3", "quote": "Differentially expressed genes (DEGs) were identified by calculating the variance from a beta binomial distribution using the method of Baggerly et al. [8] against quantile normalized observed counts [reviewed in [9]] producing per gene p-values that were false discovery rate (FDR) corrected for multiple comparison [10]."}, {"asset": "source:pmid:25478318", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "From these data (GEO accession number GSE49949), it appears that Sip1 regulates multiple genes in the lens that are generally distinct from those regulated by Sip1 in other cellular contexts, including genes whose expression is prominent in the early head ectoderm, from which the lens differentiates."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A filtering workflow reduced 7,108 statistically significant differentially expressed genes to 190 biologically relevant genes, of which 78 appeared strongly dependent on Sip1 function; differential expression was assessed using a beta-binomial variance model, and the source RNA-Seq data are available through GEO accession GSE49949.", "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:25478318"], "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:GSE32334"], "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:GSE32334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25478318", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2014.10.015", "sha256": "sha256:f17d43c6eb316f5873e0fc1e77393ee40382adbf6506519e93165b4d78a9a095", "bytes": 43074, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2014.10.015", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4248573", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32334", "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=GSE32334", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32334", "version": null, "note": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49949.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49949.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM800869", "GSM800870", "GSM800871", "GSM800872", "GSM800873", "GSM800874", "GSM800875", "GSM800876", "GSM800877", "GSM800878", "GSM800879", "GSM800880", "GSM800881", "GSM800882", "GSM800883", "GSM800884", "GSM800885", "GSM800886", "GSM800887"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Developmental timecourse of mouse ocular lens and whole embryo control", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE49949", "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=GSE49949", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE49949", "version": null, "note": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49949.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49949.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1210567", "GSM1210568", "GSM1210569", "GSM1210570", "GSM1210571", "GSM1210572", "GSM1210573", "GSM1210574", "GSM1210575"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "13112", "taxon": "Mus musculus", "title": "Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development", "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:25478318:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:edf3cc49075945ff7fd5cdc3d8d59dff46fabf3f7a4831ddd335f3b0ca3091de", "bytes": 1765, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#t0005", "version": null, "note": "Expression levels for representative regulatory and structural genes in the E15.5 inbred mouse lens.", "structure": {"pmcid": "PMC4248573", "section_index": 8, "section_title": "Filtering strategy", "row_count": 31, "column_count": 4}, "table": {"label": "Table 1", "caption": "Expression levels for representative regulatory and structural genes in the E15.5 inbred mouse lens.", "rows": [["Gene symbol", "Gene name", "Mean expression (RPKM)", "Citation"], ["Regulatory genes"], ["Bin3", "Bridging integrator 3", "2.6", "[21]"], ["Cdh1", "E-cadherin", "35.0", "[22]"], ["Dnase2B", "Deoxyribonuclease II beta", "16.9", "[23]"], ["Fgfr1", "Fibroblast growth factor receptor 1", "13.4", "[24]"], ["Fgfr2", "Fibroblast growth factor receptor 2", "9.0", "[24]"], ["Fgfr3", "Fibroblast growth factor receptor 3", "41.4", "[24]"], ["Foxe3", "Forkhead box E3", "136.4", "[25]"], ["Itga3", "α3-Integrin", "9.1", "[26]"], ["Itga6", "α6-Integrin", "27.4", "[26]"], ["Itgav", "αV-Integrin", "8.9", "[27]"], ["Itgb1", "β1-Integrin", "74.6", "[28]"], ["Jag1", "Jagged 1", "66.2", "[29]"], ["Loxl1", "Lysyl oxidase-like 1", "24.3", "[30]"], ["MAF", "Avian musculoaponeurotic fibrosarcoma AS42 oncogene homolog (c-Maf)", "152.7", "[31]"], ["NHS", "Nance –Horan Syndrome", "13.3", "[32]"], ["Notch2", "Notch gene homolog 2", "4.1", "[33]"], ["Notch 1", "Notch gene homolog 1", "2.5", "[34]"], ["Pax6", "Paired box gene 6", "11.2", "[35]"], ["Prox1", "Prospero-related homeobox 1", "97.6", "[36]"], ["Six3", "Sine oculis-related homeobox 3 homolog", "13.8", "[37]"], ["Tdrd7", "Tudor domain containing 7", "362", "[38]"], ["Txn1", "Thioredoxin 1", "66.2", "[39]"], ["Zeb1", "Zinc finger E-box binding homeobox 1 (δEF1)", "3.8", "[19]"], ["Zeb2", "Zinc finger E-box binding homeobox 2 (Sip1)", "5.8", "[1]"], [""], ["Structural genes"], ["Cryba1", "βA3/A1 crystallin", "23,643.5", "[40]"], ["Crygf", "γF-crystallin", "14,682.3", "[41]"], ["Mip", "Major intrinsic protein of the eye lens fiber (Aquaporin 0)", "3621.6", "[42]"]], "row_count": 31, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[8]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:25478318:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:50663ffbb0d0a0be1bbec54bf0bb702a7a8f388ed516b457e79d094de98f342d", "bytes": 2948, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#t0010", "version": null, "note": "Predicted biological function for genes differentially expressed more than 2.5 fold in E15.5 lenses obtained from mixed background (WT) mice compared to those from an inbred strain (AG).", "structure": {"pmcid": "PMC4248573", "section_index": 8, "section_title": "Filtering strategy", "row_count": 21, "column_count": 7}, "table": {"label": "Table 2", "caption": "Predicted biological function for genes differentially expressed more than 2.5 fold in E15.5 lenses obtained from mixed background (WT) mice compared to those from an inbred strain (AG).", "rows": [["Gene ID", "Gene name", "Fold changea", "FDR p-value", "WT RPKM meansb", "AG RPKM meansb", "Predicted biological functionc"], ["Snhg9", "Small nucleolar RNA host gene (non-protein coding) 9", "6.56", "2.52E− 05", "1.14", "7.79", "Long non-coding RNA"], ["Ccbe1", "Collagen and calcium binding EGF domains 1", "5.02", "0", "0.56", "2.98", "ECM remodeling/cell migration"], ["Eif3j", "Eukaryotic translation initiation factor 3, subunit J", "4.70", "0", "6.09", "19.64", "Component of the translation initiation complex"], ["Adamts4", "A disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4", "3.69", "5.20E − 06", "1.02", "3.93", "Degradation of the cartilage proteoglycan aggrecan"], ["Lars2", "Leucyl-tRNA synthetase 2, mitochondrial", "2.90", "9.46E − 11", "150.92", "467.79", "Leucine tRNA ligase"], ["Mid1", "Midline 1", "2.71", "1.72E − 03", "6.71", "18.49", "Protein complex anchoring to microtubules"], ["Tdg", "Thymine DNA glycosylase", "2.57", "7.95E − 14", "4.19", "16.11", "DNA mismatch repair (G/T)"], ["Rpl5", "Ribosomal protein L5", "− 2.58", "3.61E− 29", "228.60", "176.68", "rRNA maturation; 60S ribosomal subunit formation"], ["Cd59a", "CD59a antigen", "− 2.65", "6.01E− 14", "5.57", "2.09", "Complement-mediated cell lysis regulation"], ["Avp", "Arginine vasopressin", "− 2.66", "1.56E− 08", "4.94", "1.71", "Water retention; blood vessel constriction"], ["Lsm7", "LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)", "− 2.74", "8.54E− 10", "70.55", "62.08", "U6 snRNA binding during pre-mRNA splicing"], ["Ccdc117", "Coiled-coil domain containing 117", "− 2.82", "3.51E− 19", "26.31", "9.68", "Unknown"], ["Rpl22l1", "Ribosomal protein L22 like 1", "− 3.00", "6.19E− 14", "183.84", "71.56", "Protein component of the ribosome"], ["Nme2", "NME/NM23 nucleoside diphosphate kinase 2", "− 3.27", "2.28E− 10", "174.43", "132.82", "Non-ATP nucleoside triphosphate synthesis"], ["mt-Atp8", "Mitochondrially encoded ATP synthase protein 8", "− 3.28", "7.69E− 09", "2343.43", "1146.27", "Membrane anchor for ATP synthase"], ["Scg5", "Secretogranin V", "− 4.37", "3.08E− 40", "2.71", "0.61", "Molecular chaperone"], ["Gchfr", "GTP cyclohydrolase I feedback regulator", "− 4.38", "2.89E− 04", "2.96", "0.68", "Mediator of GTP cyclohydrolase inhibition"], ["Zfp580", "Zinc finger protein 580", "− 5.20", "2.22E− 03", "3.31", "1.07", "Endothelial cell proliferation and migration"], ["Xlr3b", "X-linked lymphocyte-regulated 3B", "− 5.22", "3.62E− 12", "2.59", "0.49", "Facilitator of parent-of-origin effects on cognitive function"], ["Hist1h2al", "Histone cluster 1, H2al", "–?", "0.011", "10.17", "0.71", "Core component of nucleosomes"]], "row_count": 21, "column_count": 7, "numeric_cells": 98, "header_rows": 1, "locator": "section[8]/table-wrap[2]#t0010"}}], "gaps": ["asset:data:geo:GSE32334 not downloaded", "asset:data:geo:GSE32334 licence not read", "asset:data:geo:GSE49949 not downloaded", "asset:data:geo:GSE49949 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Beta-binomial variance method of Baggerly et al., with false discovery rate correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes (DEGs) were identified by calculating the variance from a beta binomial distribution using the method of Baggerly et al. [8] against quantile normalized observed counts [reviewed in [9]] producing per gene p-values that were false discovery rate (FDR) corrected for multiple comparison [10]."}}], "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 (Beta-binomial variance method of Baggerly et al., with false discovery rate correction), 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": ["GSE49949", "GSE32334"], "resolved_accessions": ["GSE49949", "GSE32334"], "statements": ["Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49949."], "basis": "The paper names GSE49949, GSE32334 in NCBI 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:25478318", "data:geo:GSE32334", "asset:table:pmid:25478318:1", "asset:table:pmid:25478318:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32334"]}, "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": "2026-10-31T18:23:15Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 87881, "completion_tokens": 4154, "cached_tokens": 1672}}, "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:25478318", "type": "paper", "label": "pmid:25478318"}, {"id": "source:pmid:25478318", "type": "manuscript", "label": "PMID 25478318 full text"}, {"id": "data:geo:GSE32334", "type": "dataset", "label": "GEO GSE32334"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25478318", "type": "paper", "label": "pmid:25478318"}, {"id": "source:pmid:25478318", "type": "manuscript", "label": "PMID 25478318 full text"}, {"id": "data:geo:GSE32334", "type": "dataset", "label": "GEO GSE32334"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25478318", "type": "extraction", "used": ["source:pmid:25478318"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32334", "type": "accession_resolution", "used": ["data:geo:GSE32334"], "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:25478318", "parent_hash": "sha256:122021a1041b9738e7194d3fb60504c9e8ccfb5da639e88bb97cc3e82f15eaf6", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE32334 licence not read", "asset:data:geo:GSE32334 not downloaded", "asset:data:geo:GSE49949 licence not read", "asset:data:geo:GSE49949 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["pment of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens du", "-generation sequencing of the transcriptome (RNA-Seq) is a powerful method that allows for the qu", "ad interacting protein 1 (Sip1) obtained via RNA-Seq by Manthey and colleagues in Mechanisms of D", "at can be used to prioritize genes in future RNA-Seq investigations performed at this stage of oc"], "order_basis": "paper_text_order:6", "id": "assay:1"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Next-generation sequencing of the transcriptome (RNA-Seq) is a powerful"], "order_basis": "paper_text_order:130", "id": "assay:2"}]}