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Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood.
Kalikiri, Mahesh Kumar Reddy; Manjunath, Harshitha Shobha; Vempalli, Fazulur Rehaman; Mathew, Lisa Sara; Liu, Li; Wang, Li; Wang, Guishuang; Wang, Kun; Soloviov, Oleksandr; Lorenz, Stephan; Tomei, Sara.
Afiliación
  • Kalikiri MKR; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Manjunath HS; Omics Core, Integrated Genomic Services, Sidra Medicine, Doha, Qatar.
  • Vempalli FR; Bioinformatics Core, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Mathew LS; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Liu L; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Wang L; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Wang G; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Wang K; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Soloviov O; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Lorenz S; Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar.
  • Tomei S; Omics Core, Integrated Genomic Services, Sidra Medicine, Doha, Qatar.
Sci Rep ; 13(1): 3598, 2023 03 03.
Article en En | MEDLINE | ID: mdl-36869090
Transcriptome profiling of human whole blood is used to discover biomarkers of diseases and to assess phenotypic traits. Recently, finger-stick blood collection systems have allowed a less invasive and quicker collection of peripheral blood. Such non-invasive sampling of small volumes of blood offers practical advantages. The quality of gene expression data is strictly dependent on the steps used for the sample collection, extraction, preparation and sequencing. Here we have: (i) compared the manual and automated RNA extraction of small volumes of blood using the Tempus Spin RNA isolation kit and the MagMAX for Stabilized Blood RNA Isolation kit , respectively; and (ii) assessed the effect of TURBO DNA Free treatment on the transcriptomic data of RNA isolated from small volumes of blood. We have used the QuantSeq 3' FWD mRNA-Seq Library Prep kit to prepare RNA-seq libraries, which were sequenced on the Illumina NextSeq 500 system. The samples isolated manually displayed a higher variability in the transcriptomic data as compared to the other samples. The TURBO DNA Free treatment affected the RNA samples negatively, decreasing the RNA yield and reducing the quality and reproducibility of the transcriptomic data. We conclude that automated extraction systems should be preferred over manual extraction systems for data consistency, and that the TURBO DNA Free treatment should be avoided when working on RNA samples isolated manually from small volumes of blood.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Perfilación de la Expresión Génica / Gastrópodos Tipo de estudio: Guideline Límite: Animals / Humans Idioma: En Revista: Sci Rep Año: 2023 Tipo del documento: Article País de afiliación: Qatar Pais de publicación: Reino Unido

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Perfilación de la Expresión Génica / Gastrópodos Tipo de estudio: Guideline Límite: Animals / Humans Idioma: En Revista: Sci Rep Año: 2023 Tipo del documento: Article País de afiliación: Qatar Pais de publicación: Reino Unido