Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4 + T cell activation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28050347", "kind": "science-record", "revision": 8, "content_hash": "sha256:74d21d21dbebeb0f4b6c0e75c594c6d22bfc5110488c18162135e1d69a651257", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T22:42:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4 + T cell activation.", "doi": "10.1016/j.gdata.2016.12.006", "pmid": "28050347", "authors": ["Thomas C Whisenant"], "journal": "Genomics data", "year": 2017, "abstract": "CD4 T cell activation is a central component of the mammalian adaptive immune response and is underscored by a dramatic change in the gene expression profile in these cells. The changes in gene expression that occur during T cell activation are regulated in multiple ways including post-transcriptionally by complexes of RNA-binding proteins. Recently, our study explored the role of the RNA-binding protein U2AF2 and its interacting proteins in mediating posttranscriptional changes in constitutive and alternative splicing during T cell activation. First, we used RNA-seq to identify the global changes in gene expression and splicing that occur with T cell activation. Next, we used RIP-seq to identify the specific genes bound to U2AF2 during T cell activation. After identification of the protein interacting partners of U2AF2, we used splicing sensitive microarrays to measure the effects on global gene expression of using siRNAs to knock down a sampling of these proteins. Finally, we used RIP-chip to measure the effects of the same siRNA knockdown on the transcripts specifically bound to U2AF2. Here we provide the experimental details and analysis of the gene expression data for each of these techniques, which have been deposited into Gene Expression Omnibus (GEO) with the Superseries ID: GSE62923.", "claims": [{"id": "claim-method", "statement": "The read counts for the remaining genes were input into the edgeR package [5] to measure differential gene expression (FDR < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28050347", "locator": "sections[10] \"RNA-seq differential gene expression and splicing\" paragraph 2", "quote": "The read counts for the remaining genes were input into the edgeR package [5] to measure differential gene expression (FDR < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are publically available", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28050347", "locator": "sections[1] \"p\" paragraph 1", "quote": "Data are publically available"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Here we provide the experimental details and analysis of the gene expression data for each of these techniques, which have been deposited into Gene Expression Omnibus (GEO) with the Superseries ID: GSE62923.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28050347", "locator": "sections[10] \"RNA-seq differential gene expression and splicing\" paragraph 2", "quote": "The read counts for the remaining genes were input into the edgeR package [5] to measure differential gene expression (FDR < 0.05)."}, {"asset": "source:pmid:28050347", "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=GSE62923."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Here we provide the experimental details and analysis of the gene expression data for each of these techniques, which have been deposited into Gene Expression Omnibus (GEO) with the Superseries ID: GSE62923.", "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:28050347"], "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:GSE62923"], "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": {"fdr_threshold": "edgeR package with an FDR threshold of < 0"}, "inputs": ["data:geo:GSE62923"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28050347", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2016.12.006", "sha256": "sha256:21886a04391f4646fa914c8b1611d6ed75a5a461096116683172953b921cbdcf", "bytes": 17023, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2016.12.006", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5192059", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62923", "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=GSE62923", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62923", "version": null, "note": "Data are publically available", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are publically available", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1536235", "GSM1536236", "GSM1536237", "GSM1536238", "GSM1536239", "GSM1536240", "GSM1536241", "GSM1536242", "GSM1536243", "GSM1536244", "GSM1536245", "GSM1536246", "GSM1536247", "GSM1536248", "GSM1536249", "GSM1536250", "GSM1536251", "GSM1536252", "GSM1536253", "GSM1536254", "GSM1536255", "GSM1536256", "GSM1536257", "GSM1536258", "GSM1536259", "GSM1536260", "GSM1536261", "GSM1536262", "GSM1536263", "GSM1536264", "GSM1536265", "GSM1536266", "GSM1536267", "GSM1536268", "GSM1536269", "GSM1536270", "GSM1536271", "GSM1536272", "GSM1536273", "GSM1536274", "GSM1536275", "GSM1536276", "GSM1536277", "GSM1536278", "GSM1536279", "GSM1536280", "GSM1536281", "GSM1536282", "GSM1536283", "GSM1536284", "GSM1536285", "GSM1536286", "GSM1536287", "GSM1536288", "GSM1536289", "GSM1536290", "GSM1536291", "GSM1536292", "GSM1536293", "GSM1536294", "GSM1536295", "GSM1536296", "GSM1536297", "GSM1536298", "GSM1536299", "GSM1536300", "GSM1536301", "GSM1536302", "GSM1536303", "GSM1536304", "GSM1536305", "GSM1536306", "GSM1536307", "GSM1536308", "GSM1536309", "GSM1536310", "GSM1536311", "GSM1536312", "GSM1536313", "GSM1536314", "GSM1536315", "GSM1536316"], "sample_count": 82, "group_sizes": null, "group_sizes_basis": null, "platform": "17585;11154;17586", "taxon": "Homo sapiens", "title": "The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells", "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:28050347:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27e83a52908670934e222400bfed4915d0da0b0ed9f1e8c5009ac5e76ac685b7", "bytes": 1779, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0020", "version": null, "note": null, "structure": {"pmcid": "PMC5192059", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissueGenome or genomic data origin", "Human"], ["SexMale or female", "Female"], ["Sequencer or array typeType of sequencer", "Illumina HiSeq 2000 (RNA-seq), Affymetrix Human Transcriptome Array 2.0 GeneChip (Microarray)"], ["Data formatRaw or analyzed", "Raw data: fastq files (RNA-seq), CEL files (Microarray); Processed data: bam files (RNA-seq), CHP files (Microarray)"], ["Experimental factorsTumor vs. normal, any pretreatment of samples", "Resting CD4 T cell culture vs Activated CD4 T cell culture (Total RNA, U2AF2 RIP RNA); U2AF1 siRNA vs Control siRNA (Total RNA, U2AF2 RIP RNA); SYNCRIP siRNA vs Control siRNA (Total RNA, U2AF2 RIP RNA); ILF2 siRNA vs Control siRNA (Total RNA); SRRM2 siRNA vs Control siRNA (Total RNA)"], ["Experimental featuresVery brief experimental description", "RNA-seq and U2AF2 RIP-seq profiling of Resting and Activated CD4 T cell culture to identify differentially expressed/spliced and U2AF2 differentially bound genes, respectively, upon T cell Activation. Microarray gene expression profiling of Activated CD4 T cell culture to identify differentially expressed/spliced transcripts upon siRNA knockdown of RNA-binding proteins (U2AF1, SYNCRIP, ILF2, and SRRM2) relative to Control siRNA. U2AF2 RIP-chip (microarray) profiling of Activated CD4 T cell culture to identify transcripts differentially bound to U2AF2 upon siRNA knockdown of RNA-binding proteins (U2AF1 and SYNCRIP) relative to Control siRNA."], ["ConsentLevel of consent allowed for reuse", "Data are publically available"], ["Sample source locationCity, country of model organism", "La Jolla, CA, USA"]], "row_count": 9, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0020"}}], "gaps": ["asset:data:geo:GSE62923 not downloaded", "asset:data:geo:GSE62923 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fdr_threshold": "edgeR package with an FDR threshold of < 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The read counts for the remaining genes were input into the edgeR package [5] to measure differential gene expression (FDR < 0.05)."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "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": ["GSE62923"], "resolved_accessions": ["GSE62923"], "statements": ["Data are publically available"], "basis": "The paper names GSE62923 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:28050347", "data:geo:GSE62923", "asset:table:pmid:28050347:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62923"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:16Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 35719, "completion_tokens": 4053, "cached_tokens": 2096}}, "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:28050347", "type": "paper", "label": "pmid:28050347"}, {"id": "source:pmid:28050347", "type": "manuscript", "label": "PMID 28050347 full text"}, {"id": "data:geo:GSE62923", "type": "dataset", "label": "GEO GSE62923"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28050347", "type": "paper", "label": "pmid:28050347"}, {"id": "source:pmid:28050347", "type": "manuscript", "label": "PMID 28050347 full text"}, {"id": "data:geo:GSE62923", "type": "dataset", "label": "GEO GSE62923"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28050347", "type": "extraction", "used": ["source:pmid:28050347"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62923", "type": "accession_resolution", "used": ["data:geo:GSE62923"], "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:28050347", "parent_hash": "sha256:68ee5c4ac2085cabe2a8d139066a6ac535e67881f00533800d55cb03ba22cbc3", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE62923 licence not read", "asset:data:geo:GSE62923 not downloaded", "execution.not_run", "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": 0.93, "evidence": ["ing during T cell activation. First, we used RNA-seq to identify the global changes in gene expre"], "order_basis": "paper_text_order:623", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hip to measure the effects of the same siRNA knockdown on the transcripts specifically bound to U2A", "RIP-chip to measure the effects of the same siRNA knockdown on the transcripts specifically bo", "microarray experiments (Table 2), cells were transfected by Amaxa Nucleofection (Lonza) following the", "instructions (program CL-120), with specific siRNA added to a final concentration of 300 nM. Ce"], "order_basis": "paper_text_order:1100", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["T-Activator CD3/CD28 (Thermo) for 48 h, and cultured in the presence of 30 U/ml of IL2. While kept a"], "order_basis": "paper_text_order:1842", "id": "assay:3"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["unchanged for the same 48 h window. For all microarray experiments (Table 2), cells were transfecte"], "order_basis": "paper_text_order:2478", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The read counts for the remaining genes were input into the edgeR package [5] to measure differential gene expression (FDR < 0.05)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}