Endogenous circadian time genes expressions in the liver of mice under constant darkness.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32160860", "kind": "science-record", "revision": 6, "content_hash": "sha256:89e45d58489d0702f32ceb3e76630e1fc3dbf170e7836877cfcab7fae6becffb", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T21:22:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Endogenous circadian time genes expressions in the liver of mice under constant darkness.", "doi": "10.1186/s12864-020-6639-4", "pmid": "32160860", "authors": ["Huan Li", "Shiyao Zhang", "Wenxiang Zhang", "Siyu Chen", "Anjara Rabearivony", "Yujie Shi", "Jie Liu", "Christopher J Corton", "Chang Liu"], "journal": "BMC genomics", "year": 2020, "abstract": "BACKGROUND: The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6 weeks, and the liver samples were collected starting at 9:00 AM (CT1), and every 4 h in a 24-h cycle (CT5, CT9, CT13, CT17 and CT21). Total RNA was extracted and subjected to RNA-Seq data (deposited as GSE 133342, L-DD). To compare gene oscillation pattern under normal light-dark condition (LD, GSE114400) and short time (2 days) dark-dark condition (S-DD, GSE70497), these data were retried from GEO database, and the trimmed mean of M-values normalization was used to normalize the three RNA-seq data followed by MetaCycle analysis.\nRESULTS: Approximate 12.1% of the genes under L-DD exhibited significant rhythmically expression. The top 5 biological processes enriched in L-DD oscillation genes were mRNA processing, aromatic compound catabolic process, mitochondrion organization, heterocycle catabolic process and cellular nitrogen compound mitotic catabolic process. The endogenous circadian rhythms of clock genes, P450 genes and lipid metabolism genes under L-DD were further compared with LD and S-DD. The oscillation patterns were similar but the period and amplitude of those oscillation genes were slightly altered. RT-qPCR confirmed the selected RNA sequence findings.\nCONCLUSIONS: This is the first study to profile oscillation gene expressions under L-DD. Our data indicate that clock genes, P450 genes and lipid metabolism genes expressed rhythmically under L-DD. Light was not the necessary factor for persisting circadian rhythm but influenced the period and amplitude of oscillation genes.", "claims": [{"id": "claim-method", "statement": "Student’s t test was used to compare the differences between CT1 and the other time points.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32160860", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "Student’s t test was used to compare the differences between CT1 and the other time points."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32160860", "locator": "sections[18] \"Availability of data and materials\" paragraph 2", "quote": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi."}], "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:32160860"], "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:GSE114400"], "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:GSE114400"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32160860", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-020-6639-4", "sha256": "sha256:650003e44af295df3804db3f895df5f89fcd4c2da74413f0cfbfca9a25d782cb", "bytes": 47446, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12864-020-6639-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7066782", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE114400", "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=GSE114400", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE114400", "version": null, "note": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2046155", "GSM2046156", "GSM2046157", "GSM2046158", "GSM2046159", "GSM2046160", "GSM2046179", "GSM2046180", "GSM2046181", "GSM2046182", "GSM2046183", "GSM2046184", "GSM2046202", "GSM2046203", "GSM2046204", "GSM2046205", "GSM2046206", "GSM2046207", "GSM2046223", "GSM2046224", "GSM2046225", "GSM2046226", "GSM2046227", "GSM2046228", "GSM2355588", "GSM2355589", "GSM2355590", "GSM2355591", "GSM2355592", "GSM2355593", "GSM2355594", "GSM2355595", "GSM2355596", "GSM2355597", "GSM2355598", "GSM2355599", "GSM2355600", "GSM2355601", "GSM2355602", "GSM2355603", "GSM2355604", "GSM2355605", "GSM2355606", "GSM2355607", "GSM2355608", "GSM2355609", "GSM2355610", "GSM2355611"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "17021", "taxon": "Mus musculus", "title": "Temporal profiles of germ-free and conventionally raised female and male mice (LIVER)", "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:GSE133342", "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=GSE133342", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE133342", "version": null, "note": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3906007", "GSM3906008", "GSM3906009", "GSM3906010", "GSM3906011", "GSM3906012", "GSM3906013", "GSM3906014", "GSM3906015"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "21493", "taxon": "Mus musculus", "title": "Angptl8 mediates food-driven resetting of hepatic circadian clock in mice", "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:GSE70497", "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=GSE70497", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70497", "version": null, "note": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1787223", "GSM1787224", "GSM1787226", "GSM1787227", "GSM1787228", "GSM1787229", "GSM1787230", "GSM1787231", "GSM1787232", "GSM1787234", "GSM1787235", "GSM1787236", "GSM1787237", "GSM1787238", "GSM1787239", "GSM1787241", "GSM1787242", "GSM1787243", "GSM1787244", "GSM1787245", "GSM1787246", "GSM1787248", "GSM1787249", "GSM1787250", "GSM1787251", "GSM1787252", "GSM1787253", "GSM1787255", "GSM1787256", "GSM1787257", "GSM1787258", "GSM1787259", "GSM1787260", "GSM1787261", "GSM1787263", "GSM1787264", "GSM1787265", "GSM1787266", "GSM1787267", "GSM1787268", "GSM1787270", "GSM1787271", "GSM1787272", "GSM1787273", "GSM1787275", "GSM1787276", "GSM1787277", "GSM1787278"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "13112", "taxon": "Mus musculus", "title": "Effect of Bmal1 post-natal knockout on liver gene expression: time-series", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32160860:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f3137df6960508028a2f09f1bfb1dd15435fda1115b0b57a3181d6813c18c871", "bytes": 1323, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#Tab1", "version": null, "note": "Comparisons of hepatic circadian clock genes under LD, S-DD and L-DD conditions", "structure": {"pmcid": "PMC7066782", "section_index": 2, "section_title": "Results", "row_count": 15, "column_count": 10}, "table": {"label": "Table 1", "caption": "Comparisons of hepatic circadian clock genes under LD, S-DD and L-DD conditions", "rows": [["Name", "P-value", "Period (hour)", "_rAmplitude"], ["LD", "S-DD", "L-DD", "LD", "S-DD", "L-DD", "LD", "S-DD", "L-DD"], ["Bmal1", "0.07", "0.00", "0.28", "21.56", "22.06", "22.47", "0.51", "0.68", "0.50"], ["Clock", "0.01", "0.00", "0.48", "20.33", "20.93", "23.25", "0.08", "0.13", "0.06"], ["Npas2", "0.02", "0.00", "0.01", "22.06", "21.14", "24.45", "2.25", "3.86", "2.50"], ["Per1", "0.05", "0.00", "0.01", "21.00", "22.56", "24.96", "0.62", "0.54", "0.95"], ["Per2", "0.08", "0.01", "0.00", "20.16", "22.95", "21.03", "0.39", "0.42", "0.40"], ["per3", "0.01", "0.00", "0.03", "22.73", "23.4", "22.86", "0.29", "0.47", "0.72"], ["Cry1", "0.17", "0.02", "0.04", "21.59", "23.05", "23.31", "0.28", "0.30", "0.26"], ["Cry2", "0.22", "0.14", "0.04", "25.54", "24.78", "20.05", "0.08", "0.06", "0.15"], ["Rev-erbα", "0.17", "0.04", "0.15", "21.97", "22.55", "21.33", "0.64", "0.65", "1.07"], ["Rev-erbβ", "0.01", "0.00", "0.08", "20.19", "22.41", "22.62", "0.16", "0.26", "0.19"], ["Dbp", "0.02", "0.00", "0.24", "22.11", "20.90", "20.61", "0.46", "0.95", "0.85"], ["Tef", "0.02", "0.00", "0.04", "22.73", "21.70", "24.10", "0.13", "0.19", "0.28"], ["Hlf", "0.04", "0.02", "0.02", "20.12", "22.34", "20.02", "0.11", "0.06", "0.19"]], "row_count": 15, "column_count": 10, "numeric_cells": 117, "header_rows": 2, "locator": "section[2]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32160860:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bb81d85491f2152d270c60fae34f85c3b80920eeaa706c67dafab7e317cbb594", "bytes": 1188, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[2]#Tab2", "version": null, "note": "Comparisons of hepatic cytochrome P450 genes under LD, S-DD and L-DD conditions", "structure": {"pmcid": "PMC7066782", "section_index": 2, "section_title": "Results", "row_count": 13, "column_count": 10}, "table": {"label": "Table 2", "caption": "Comparisons of hepatic cytochrome P450 genes under LD, S-DD and L-DD conditions", "rows": [["Name", "P-value", "Period (hour)", "rAmplitude"], ["LD", "S-DD", "L-DD", "LD", "S-DD", "L-DD", "LD", "S-DD", "L-DD"], ["Cyp1a1", "0.14", "0.83", "0.05", "23.59", "25.33", "23.02", "0.19", "0.15", "0.39"], ["Cyp2a4", "0.01", "0.04", "0.05", "22.44", "20.12", "20.34", "1.21", "0.19", "0.52"], ["Cyp2a5", "0.01", "0.01", "0.02", "22.74", "24.32", "25.57", "0.17", "0.16", "0.22"], ["Cyp2b10", "0.81", "0.02", "0.06", "21.33", "22.76", "25.18", "0.97", "0.13", "0.46"], ["Cyp2c29", "0.50", "0.87", "0.03", "24.45", "21.33", "25.34", "0.01", "0.05", "0.05"], ["Cyp2d40", "0.01", "0.94", "0.03", "25.26", "24.00", "20.28", "0.06", "0.06", "0.07"], ["Cyp2e1", "0.03", "0.09", "0.00", "21.71", "24.45", "23.92", "0.03", "0.04", "0.05"], ["Cyp2g1", "0.00", "0.06", "0.01", "22.91", "20.31", "22.48", "0.88", "0.61", "1.12"], ["Cyp4a14", "0.66", "0.11", "0.04", "21.63", "20.23", "20.34", "0.16", "0.05", "0.54"], ["Cyp51", "0.15", "0.57", "0.02", "20.51", "21.33", "25.33", "0.09", "0.04", "0.06"], ["Cyp7a1", "0.82", "0.05", "0.04", "21.33", "21.33", "22.86", "0.13", "0.13", "0.15"]], "row_count": 13, "column_count": 10, "numeric_cells": 104, "header_rows": 2, "locator": "section[2]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:32160860:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8f54b38a6a7241ad14457df36ce1d02c7bcd751276749b530f5bd6b98d96ded1", "bytes": 1269, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[3]#Tab3", "version": null, "note": "Comparisons of hepatic cholesterol and fatty acids metabolism genes under LD, S-DD and L-DD conditions", "structure": {"pmcid": "PMC7066782", "section_index": 2, "section_title": "Results", "row_count": 14, "column_count": 10}, "table": {"label": "Table 3", "caption": "Comparisons of hepatic cholesterol and fatty acids metabolism genes under LD, S-DD and L-DD conditions", "rows": [["Name", "P-value", "Priod (hour)", "rAmplitude"], ["LD", "S-DD", "L-DD", "LD", "S-DD", "L-DD", "LD", "S-DD", "L-DD"], ["Hmgcs1", "0.05", "NA", "0.02", "20.02", "NA", "25.02", "0.19", "NA", "0.13"], ["Acot3", "0.00", "0.01", "0.01", "22.19", "20.05", "20.69", "1.07", "0.20", "1.77"], ["Acot4", "0.01", "0.04", "0.02", "22.48", "20.19", "20.41", "0.18", "0.08", "0.24"], ["Acot8", "0.35", "0.19", "0.02", "21.87", "22.89", "20.37", "0.04", "0.03", "0.06"], ["Acot13", "0.00", "0.11", "0.00", "22.80", "25.29", "22.64", "0.04", "0.03", "0.07"], ["Lpin1", "0.04", "0.00", "0.00", "20.22", "22.62", "20.95", "0.21", "0.17", "0.25"], ["Lpin2", "0.02", "0.01", "0.01", "22.03", "22.12", "24.32", "0.08", "0.07", "0.10"], ["Scd1", "0.40", "0.05", "0.60", "25.33", "23.57", "22.15", "0.01", "0.02", "0.03"], ["Scd2", "0.00", "0.03", "0.70", "22.69", "22.99", "21.33", "0.05", "0.07", "0.14"], ["Thrsp", "0.45", "0.06", "0.00", "24.19", "23.11", "21.30", "0.06", "0.17", "0.21"], ["Angptl3", "0.03", "0.91", "0.01", "23.73", "24.00", "24.87", "0.02", "0.00", "0.07"], ["Angptl4", "0.03", "0.43", "0.07", "24.05", "20.12", "23.16", "0.10", "0.09", "0.07"]], "row_count": 14, "column_count": 10, "numeric_cells": 106, "header_rows": 2, "locator": "section[2]/table-wrap[3]#Tab3"}}], "gaps": ["asset:data:geo:GSE114400 not downloaded", "asset:data:geo:GSE114400 licence not read", "asset:data:geo:GSE133342 not downloaded", "asset:data:geo:GSE133342 licence not read", "asset:data:geo:GSE70497 not downloaded", "asset:data:geo:GSE70497 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Student’s t test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student’s t test was used to compare the differences between CT1 and the other time points."}}], "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 (Student’s t test), 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": ["GSE114400", "GSE70497", "GSE133342"], "resolved_accessions": ["GSE114400", "GSE70497", "GSE133342"], "statements": ["Three sets of RNA-seq data (Accession number: GSE114400, GSE70497, GSE133342) generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi."], "basis": "The paper names GSE114400, GSE70497, GSE133342 in GEO repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32160860", "data:geo:GSE114400", "asset:table:pmid:32160860:1", "asset:table:pmid:32160860:2", "asset:table:pmid:32160860:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE114400"]}, "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": "2026-10-31T18:18:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 38489, "completion_tokens": 1490, "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:32160860", "type": "paper", "label": "pmid:32160860"}, {"id": "source:pmid:32160860", "type": "manuscript", "label": "PMID 32160860 full text"}, {"id": "data:geo:GSE114400", "type": "dataset", "label": "GEO GSE114400"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32160860", "type": "paper", "label": "pmid:32160860"}, {"id": "source:pmid:32160860", "type": "manuscript", "label": "PMID 32160860 full text"}, {"id": "data:geo:GSE114400", "type": "dataset", "label": "GEO GSE114400"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32160860", "type": "extraction", "used": ["source:pmid:32160860"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE114400", "type": "accession_resolution", "used": ["data:geo:GSE114400"], "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:32160860", "parent_hash": "sha256:92381effbefd79e9908efa3df48a46486655379a03b66d9fcc050b060da837bf", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE114400 licence not read", "asset:data:geo:GSE114400 not downloaded", "asset:data:geo:GSE133342 licence not read", "asset:data:geo:GSE133342 not downloaded", "asset:data:geo:GSE70497 licence not read", "asset:data:geo:GSE70497 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.99, "evidence": ["expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for", "e bright light influence before experiments. Mice were sacrificed by dislocation of the cervical vertebrae. Li", "l University (Permit number SYXK-2018-0019). Mice were housed for 1-week acclimation under a 12:12-", ", XieTong Organism, China). Subsequently, 42 mice were randomly divided into six groups, and each g"], "order_basis": "paper_text_order:312", "id": "assay:1"}, {"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": ["1). Total RNA was extracted and subjected to RNA-Seq data (deposited as GSE 133342, L-DD). To com", "ormalization was used to normalize the three RNA-seq data followed by MetaCycle analysis. RESULTS", "lability of data and materials Three sets of RNA-seq data (Accession number: GSE114400, GSE70497,", "tional file 1. Oscillation genes under L-DD. RNA-Seq data of L-DD was subjected to MetaCycle to s"], "order_basis": "paper_text_order:542", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ose oscillation genes were slightly altered. RT-qPCR confirmed the selected RNA sequence findings", "oscillation genes were slightly altered. RT-qPCR confirmed the selected RNA sequence findings", "T13, CT17 and CT21. Statistical analysis The RT-qPCR data was presented as group mean with SEM (n", ", CT17 and CT21. Statistical analysis The RT-qPCR data was presented as group mean with SEM (n"], "order_basis": "paper_text_order:1497", "id": "assay:3"}]}