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Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms.
Li, Hongyang; Eksi, Ridvan; Yi, Daiyao; Godfrey, Bradley; Mathew, Lisa R; O'Connor, Christopher L; Bitzer, Markus; Kretzler, Matthias; Menon, Rajasree; Guan, Yuanfang.
Afiliação
  • Li H; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Eksi R; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Yi D; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Godfrey B; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Mathew LR; Harvard College, Cambridge, Massachusetts, United States of America.
  • O'Connor CL; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Bitzer M; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Kretzler M; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Menon R; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
  • Guan Y; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
PLoS Comput Biol ; 18(4): e1010040, 2022 04.
Article em En | MEDLINE | ID: mdl-35468141
Studying isoform expression at the microscopic level has always been a challenging task. A classical example is kidney, where glomerular and tubulo-interstitial compartments carry out drastically different physiological functions and thus presumably their isoform expression also differs. We aim at developing an experimental and computational pipeline for identifying isoforms at microscopic structure-level. We microdissected glomerular and tubulo-interstitial compartments from healthy human kidney tissues from two cohorts. The two compartments were separately sequenced with the PacBio RS II platform. These transcripts were then validated using transcripts of the same samples by the traditional Illumina RNA-Seq protocol, distinct Illumina RNA-Seq short reads from European Renal cDNA Bank (ERCB) samples, and annotated GENCODE transcript list, thus identifying novel transcripts. We identified 14,739 and 14,259 annotated transcripts, and 17,268 and 13,118 potentially novel transcripts in the glomerular and tubulo-interstitial compartments, respectively. Of note, relying solely on either short or long reads would have resulted in many erroneous identifications. We identified distinct pathways involved in glomerular and tubulo-interstitial compartments at the isoform level, creating an important experimental and computational resource for the kidney research community.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Ano de publicação: 2022 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Ano de publicação: 2022 Tipo de documento: Article