{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Omidsalar AA"],"funding":["NIA NIH HHS","NIMH NIH HHS","NINDS NIH HHS"],"pagination":["200"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10874445"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["7(1)"],"pubmed_abstract":["Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correla"],"journal":["Communications biology"],"pubmed_title":["Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets."],"pmcid":["PMC10874445"],"funding_grant_id":["U24 NS072026","R01 MH085801","U01 NS120260","P30 AG019610","R21 MH113177","P30 AG072980"],"pubmed_authors":["Xu L","Vawter MP","Webb MG","Sequeira A","Limon A","Serrano GE","Omidsalar AA","Lew MF","McCullough CG","Santorelli M","Boedijono S","Hjelm BE","Manojlovic Z","Beach TG","Gerke D"],"additional_accession":[]},"is_claimable":false,"name":"Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets.","description":"Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correla","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Feb","modification":"2026-06-17T06:34:59.586Z","creation":"2025-04-19T07:36:10.982Z"},"accession":"S-EPMC10874445","cross_references":{"pubmed":["38368460"],"doi":["10.1038/s42003-024-05877-4"]}}