Transcriptome analysis of the aquaporin AtPIP1;2 deficient line in Arabidopsis thaliana.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484207", "kind": "science-record", "revision": 6, "content_hash": "sha256:5c2d67af29acc1555f1430780996d5ce9697d2140f8dee498364eecc46c4593c", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T21:20:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome analysis of the aquaporin AtPIP1;2 deficient line in Arabidopsis thaliana.", "doi": "10.1016/j.gdata.2015.04.018", "pmid": "26484207", "authors": ["Anastassia Boudichevskaia", "Marlies Heckwolf", "Lea Althaus", "Ralf Kaldenhoff"], "journal": "Genomics data", "year": 2015, "abstract": "Atmospheric CO2 impacts all aspects of plant development. It has changed in the past and is predicted to change further on. Studies on the response of crop plants to low and elevated CO2 concerning growth, productivity and physiological processes are intense. In contrast, the molecular mechanisms of cellular CO2 exchange are still under discussion. At the same time it becomes more and more accepted that carbon dioxide is transported across cellular biomembranes by CO2 conducting aquaporins. Our recent study (Boudichevskaia et al., 2015) demonstrates that the lack of a single gene product - aquaporin AtPIP1;2 - resulted in massive transcriptional reprogramming in Arabidopsis as a consequence of reduced tissue CO2 diffusion rates. Therefore, the transcriptome data of the aquaporin AtPIP1;2 deficient line can be used in the comparative expression analyses for better understanding the role of aquaporins with regard to CO2 and water transport in plants. Here we describe a gene expression dataset generated for three biological replicates per genotype on Affymetrix platform. We provide detailed methods and analysis on microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE62167. Additionally, we provide the R code for data preprocessing and quality control.", "claims": [{"id": "claim-method", "statement": "Statistical analyses including t-test and false discovery rate (FDR) correction [6] are described in [3].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484207", "locator": "sections[4] \"Data analysis\" paragraph 2", "quote": "Statistical analyses including t-test and false discovery rate (FDR) correction [6] are described in [3]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62167.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484207", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62167."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports 3,014 significantly regulated genes identified using a parametric t-test with false discovery rate correction, based on CEL and CHP source files deposited in GEO under accession GSE62167.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "All genes with FDR corrected p-value < 0.05 were identified as significant (Supporting file 2)."}, "evidence": [{"asset": "source:pmid:26484207", "locator": "sections[4] \"Data analysis\" paragraph 2", "quote": "The CEL files together with the corresponding CHP files were deposited on GEO under the accession number GSE62167."}, {"asset": "source:pmid:26484207", "locator": "sections[4] \"Data analysis\" paragraph 2", "quote": "Statistical analyses including t-test and false discovery rate (FDR) correction [6] are described in [3]."}, {"asset": "source:pmid:26484207", "locator": "sections[4] \"Data analysis\" paragraph 2", "quote": "All genes with FDR corrected p-value < 0.05 were identified as significant (Supporting file 2)."}, {"asset": "source:pmid:26484207", "locator": "sections[4] \"Data analysis\" paragraph 2", "quote": "Totally, of the 27,197 genes quantified by microarray 3014 genes were scored as significantly regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports 3,014 significantly regulated genes identified using a parametric t-test with false discovery rate correction, based on CEL and CHP source files deposited in GEO under accession GSE62167.", "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:26484207"], "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:GSE62167"], "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:GSE62167"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484207", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.04.018", "sha256": "sha256:4eb3ebbf4d6819a198e2ab55bbe676bdc6b9f342df38adff328ee196e92736a9", "bytes": 10417, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.04.018", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4535893", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62167", "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=GSE62167", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62167", "version": null, "note": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62167.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62167.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1520876", "GSM1520877", "GSM1520878", "GSM1520879", "GSM1520880", "GSM1520881"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "17416", "taxon": "Arabidopsis thaliana", "title": "Expression data from the T-DNA insertion line atpip1;2-1", "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:26484207:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:caed1d339ba80e16de3f332b3561ab883e0a3a1c8071eaaeda7d8f334e805e54", "bytes": 831, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t0005", "version": null, "note": "Analysis of genes significantly regulated in the mutant line atpip1;2-1 based on the GeneChip® AraGene-1.0 ST arrays (Affymetrix). The information about the whole gene number and amount of genes after removal of outliers is represented. The data are based on three biological replicates. The differentially expressed genes were determined with the parametric t-test and further corrected for multiple comparisons (FDR with p-value cutoff of < 0.05).", "structure": {"pmcid": "PMC4535893", "section_index": 4, "section_title": "Data analysis", "row_count": 4, "column_count": 6}, "table": {"label": "Table 1", "caption": "Analysis of genes significantly regulated in the mutant line atpip1;2-1 based on the GeneChip® AraGene-1.0 ST arrays (Affymetrix). The information about the whole gene number and amount of genes after removal of outliers is represented. The data are based on three biological replicates. The differentially expressed genes were determined with the parametric t-test and further corrected for multiple comparisons (FDR with p-value cutoff of < 0.05).", "rows": [["Total amount of genes", "Amount of differentially expressed genes"], ["Before filtering", "After filtering", "Up-regulated", "Down-regulated"], ["Total", "≥ Two-fold", "Total", "≥ Two-fold"], ["28,387", "27,197", "1550", "83", "1464", "91"]], "row_count": 4, "column_count": 6, "numeric_cells": 6, "header_rows": 3, "locator": "section[4]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE62167 not downloaded", "asset:data:geo:GSE62167 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Parametric t-test with false discovery rate (FDR) correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analyses including t-test and false discovery rate (FDR) correction [6] are described in [3]."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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 (Parametric t-test with false discovery rate (FDR) 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": ["GSE62167"], "resolved_accessions": ["GSE62167"], "statements": ["The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62167."], "basis": "The paper names GSE62167 in 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:26484207", "data:geo:GSE62167", "asset:table:pmid:26484207:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62167"]}, "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": "2026-10-31T18:25:30Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 25426, "completion_tokens": 2555, "cached_tokens": 1568}}, "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:26484207", "type": "paper", "label": "pmid:26484207"}, {"id": "source:pmid:26484207", "type": "manuscript", "label": "PMID 26484207 full text"}, {"id": "data:geo:GSE62167", "type": "dataset", "label": "GEO GSE62167"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484207", "type": "paper", "label": "pmid:26484207"}, {"id": "source:pmid:26484207", "type": "manuscript", "label": "PMID 26484207 full text"}, {"id": "data:geo:GSE62167", "type": "dataset", "label": "GEO GSE62167"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484207", "type": "extraction", "used": ["source:pmid:26484207"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62167", "type": "accession_resolution", "used": ["data:geo:GSE62167"], "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:26484207", "parent_hash": "sha256:69341d0058f776c1b7277e5e6c8245b505d3ddd96c341306562cb1d372791c71", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE62167 licence not read", "asset:data:geo:GSE62167 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["We provide detailed methods and analysis on microarray data which has been deposited in Gene Expres", "three biological replicates per genotype on Affymetrix platform. We provide detailed methods and an", "terial of three week-old plants was used for microarray analysis. Total RNA was isolated from 5 indi", "s isolated from 5 individual plants for each microarray (15 plants from each line in total) using th"], "order_basis": "paper_text_order:1109", "id": "assay:1"}]}