RNA-Seq data of ALKBH5 and FTO double knockout HEK293T human cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35516002", "kind": "science-record", "revision": 5, "content_hash": "sha256:7d24a279f798c460f842b9560a5b582bfc311d90bac4049ed1d4fa1e9c9e606c", "created_at": "2026-11-01T18:14:24Z", "updated_at": "2026-11-01T22:49:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RNA-Seq data of ALKBH5 and FTO double knockout HEK293T human cells.", "doi": "10.1016/j.dib.2022.108187", "pmid": "35516002", "authors": ["Egor A Smolin", "Andrey I Buyan", "Dmitry N Lyabin", "Ivan V Kulakovskiy", "Irina A Eliseeva"], "journal": "Data in brief", "year": 2022, "abstract": "N6-methyladenosine (m6A) is the most abundant, highly dynamic mRNA modification that regulates mRNA splicing, stability, and translation. The m6A epigenetic mark is erased by RNA demethylases ALKBH5 (AlkB Homolog 5) and FTO (Fat mass and obesity-associated protein). The ALKBH5 and FTO RNA demethylases recognize m6A in similar nucleotide contexts. Therefore, these proteins can partially substitute for each other. To assess the impact of total m6A demethylation failure we performed high-throughput sequencing of cytoplasmic RNA from ALKBH5 and FTO double knockout and wild type HEK293T cells. The RNA-Seq libraries were sequenced on Illumina NextSeq 500, trimmed, and mapped to the human genome. The consequent read counting and differential expression analysis in the R environment detected 5871 differentially expressed and 166 alternatively spliced genes comparing double knockout against wild type HEK293T cells. Raw data are deposited in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE198050.", "claims": [{"id": "claim-method", "statement": "Next, we used edgeR (v.3.28.1) [15] to identify differentially expressed genes among 13718 genes that passed 2 cpm for at least 3 of 6 samples for DE (default TMM-normalization with calcNormFactors, dispersion estimation with estimateDisp, and test for differential expression with exactTest).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35516002", "locator": "sections[10] \"Gene counting, differential expression, and exon usage analyses\" paragraph 2", "quote": "Next, we used edgeR (v.3.28.1) [15] to identify differentially expressed genes among 13718 genes that passed 2 cpm for at least 3 of 6 samples for DE (default TMM-normalization with calcNormFactors, dispersion estimation with estimateDisp, and test for differential expression with exactTest)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Transcriptome (RNA-Seq) of HEK293T, HEK293T ΔALKBH5ΔFTO cells (Original data) (NCBI Gene Expression Omnibus (GEO)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35516002", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "Transcriptome (RNA-Seq) of HEK293T, HEK293T ΔALKBH5ΔFTO cells (Original data) (NCBI Gene Expression Omnibus (GEO))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The consequent read counting and differential expression analysis in the R environment detected 5871 differentially expressed and 166 alternatively spliced genes comparing double knockout against wild type HEK293T cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35516002", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The consequent read counting and differential expression analysis in the R environment detected 5871 differentially expressed and 166 alternatively spliced genes comparing double knockout against wild type HEK293T cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The consequent read counting and differential expression analysis in the R environment detected 5871 differentially expressed and 166 alternatively spliced genes comparing double knockout against wild type HEK293T cells.", "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:35516002"], "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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The RNA-Seq libraries were sequenced on Illumina NextSeq", "The presented RNA-Seq data are suitable for analysis of differenti", "icantly downregulated (Fig. 2B,C). Thus, the RNA-Seq data confirm the knockout effect, and are su"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["humidified atmosphere containing 5% CO2 and passaged by standard methods. 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