Endre søk
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
Vise andre og tillknytning
Rekke forfattare: 182023 (engelsk)Inngår i: Nature Communications, E-ISSN 2041-1723, Vol. 14, nr 1, artikkel-id 509Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins. Spatial transcriptomics relies on RNA quality, which is variable and dependent on sample handling, storage, and/or intrinsic factors. Here, authors present a genome-wide spatial gene expression profiling method called RNA Rescue Spatial Transcriptomics (RRST), designed for the analysis of moderate to low quality fresh frozen tissue samples and demonstrate its robustness on 7 different tissue types.

sted, utgiver, år, opplag, sider
2023. Vol. 14, nr 1, artikkel-id 509
HSV kategori
Identifikatorer
URN: urn:nbn:se:su:diva-230433DOI: 10.1038/s41467-023-36071-5ISI: 001026236800009PubMedID: 36720873Scopus ID: 2-s2.0-85147171092OAI: oai:DiVA.org:su-230433DiVA, id: diva2:1867427
Tilgjengelig fra: 2024-06-10 Laget: 2024-06-10 Sist oppdatert: 2025-02-20bibliografisk kontrollert

Open Access i DiVA

Fulltekst mangler i DiVA

Andre lenker

Forlagets fulltekstPubMedScopus

Person

Firsova, Alexandra B.Samakovlis, Christos

Søk i DiVA

Av forfatter/redaktør
Mirzazadeh, RezaLarsson, LudvigNewton, Phillip T.Galicia, Leire AlonsoAbalo, Xesus M.Kvastad, LindaFirsova, Alexandra B.Samakovlis, Christos
Av organisasjonen
I samme tidsskrift
Nature Communications

Søk utenfor DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric

doi
pubmed
urn-nbn
Totalt: 60 treff
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf