Erratum: Near-optimal probabilistic RNA-seq quantification

Bray, Nicolas; Pimentel, Harold; Melsted, Páll; Pachter, Lior

doi:10.1038/nbt0816-888d

Cited by 257 publications

(195 citation statements)

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“…Libraries were sequenced on Hiseq 4000 (50bp reads) Gene expression levels were quantitated using kallisto [39] . These data were converted to counts and summarized per gene using tximport [40] and differential expression was carried out using DESeq2 [41] using an FDR of 0.05 and no explicit fold change cutoff.…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

Co-regulation of transcription by BRG1 and BRM, two mutually exclusive SWI/SNF ATPase subunits

Raab

Runge

Spear

et al. 2017

Preprint

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Section: Rna-seq Data Analysismentioning

confidence: 99%

Co-regulation of transcription by BRG1 and BRM, two mutually exclusive SWI/SNF ATPase subunits

Raab

Runge

Spear

et al. 2017

Preprint

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“…Danio rerio Gene Stable IDs were translated to Mus musculus Gene Stable IDs using biomaRt 51 package and the overall gene expression was analyzed with Gene Set Enrichment Analysis (GSEA) 52 using the Hallmarks collection as biological insight. Only data with adjusted p-value and FDR < 0.05 were considered significant and represented.…”

Section: Methodsmentioning

confidence: 99%

Respiratory supercomplexes provide metabolic efficiency in zebrafish

García-Poyatos

Cogliati

Hernansanz-Agustín

et al. 2019

Preprint

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or J.A. 13 Enríquez (jaenriquez@cnic.es). 14 15 16 17The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the 18 respiratory complexes coexist with super-assembled quaternary structures called 19 supercomplexes (SCs). The physiological role of SCs is still disputed. Here we used zebrafish to 20 study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-21 independent proteomics to characterize these structures and found similar SCs to those 22 described in mice, as well as novel SCs including III2+IV2, I+IV and I+III2+IV2. To study the 23 physiological role of SCs, we generated two null allele zebrafish lines for supercomplex 24 assembly factor 1 (SCAF1). SCAF1 -/fish displayed altered OXPHOS activity due to the 25 disrupted interaction of complex III and IV. SCAF1 -/fish were smaller in size, and showed 26 abnormal fat deposition and decreased female fertility. These physiological phenotypes were 27 rescued by doubling the food supply, which correlated with improved bioenergetics and 28 alterations in the metabolic gene expression program. These results reveal that SC assembly by 29 SCAF1 modulates OXPHOS efficiency and allows for the optimization of metabolic resources. 30In the last two years, the focus of investigation on the structure of the mitochondrial electron 31 transport chain (ETC) has shifted from the dispute over the existence of supercomplexes (SCs) to 32 their putative functional role. In mammals, the best understood mechanism of respiratory complex 33 super-assembly is the interaction between complexes III (CIII) and IV (CIV) mediated by 34 supercomplex assembly factor 1 (SCAF1/COX7A2L) 1 . The carboxy-terminus of SCAF1 is very 35 similar to that of the CIV subunit COX7A2 and replaces it in the subset of CIV molecules that super-36 assemble with CIII 2 . After some initial doubts 3 , which were later dispelled 4,5 , the role of SCAF1 in 37 the super-assembly of CIII and CIV is now generally accepted 2 . The process of super-assembly 38 between CI and CIII and CI and CIV to form the respirasome is unknown, but the proposed existence 39 of I+IV SCs 6 suggests that CI-CIII and CI-CIV super-assembly might occur independent from CIII 40 and CIV assembly 7,8 . So far, the interaction between CI and CIV has been mostly studied in SCs 41 containing CI, CIII and CIV (also named respirasomes). Several forms of respirasomes (I+III2+IV) 42 migrate closely together in blue native gel electrophoresis (BNGE), although the reason for their 43 SCAF1 protein (SCAF1 111 ) lacking two amino acids as compared with functional SCAF1 63 (SCAF1 113 ). SCAF1 111 mice do not assemble III2+IV and the formation of respirasomes is affected 1,2 . 64No specific phenotype has yet been ascribed to SCAF1 111 mouse strains, and this has contributed to 65 the arguments against a physiological role for the super-assembly of CIII and CIV. Furthermore, a 66 recent study performed in cultured cells suggested that the ablation of SCAF1 has no bioenergetic 67 relevance 17 , a conclusio...

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“…In addition to the reconstruction of transcript sequences, RNA sequencing also allows the user to quantify transcript expression by counting the number of sequenced reads that map to a 220 given transcript. Paired reads for each library were pseudo-aligned on the Transcriptome de Bruijn Graph (T-DBG) using Kallisto [35]. We chose this method, based on a k-mer approach, because it is much faster while providing the same accuracy as the best mapping approaches [35].…”

Section: Differential Expression and Go Enrichmentmentioning

confidence: 99%

“…Paired reads for each library were pseudo-aligned on the Transcriptome de Bruijn Graph (T-DBG) using Kallisto [35]. We chose this method, based on a k-mer approach, because it is much faster while providing the same accuracy as the best mapping approaches [35]. This method produced raw counts and normalized count statistics (TPM, or transcripts per million reads) for each assembled contig.…”

Section: Differential Expression and Go Enrichmentmentioning

confidence: 99%

“…Our study illustrates the importance of analysing the transcriptome at the level of the whole body to gain additional insights into how gene expression changes over the life cycle of an organism. Our comparison of several RNAseq datasets shows the power of transcriptomic data to accurately characterize genetic polymorphism 35 and for comparing different populations or sources of sequencing material.…”

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