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Sökning: WFRF:(Franzén Lovisa) > (2023)

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1.
  • Bhalla, Nayanika, et al. (författare)
  • Spatial transcriptomics of human placentas reveal distinct RNA patterns associated with morphology and preeclampsia
  • 2023
  • Ingår i: Placenta. - : Elsevier BV. - 0143-4004 .- 1532-3102. ; 139, s. 213-216
  • Tidskriftsartikel (refereegranskat)abstract
    • Spatial transcriptomics (ST) maps RNA level patterns within a tissue. This technology has not been previously applied to human placental tissue. We demonstrate analysis of human placental samples with ST. Unsupervised clustering revealed that distinct RNA patterns were found corresponding to different morphological structures. Additionally, when focusing upon terminal villi and hemoglobin associated structures, RNA levels differed between placentas from full term healthy pregnancies and those complicated by preeclampsia. The results from this study can provide a benchmark for future ST studies in placenta.
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2.
  • Larsson, Ludvig, et al. (författare)
  • Semla : a versatile toolkit for spatially resolved transcriptomics analysis and visualization
  • 2023
  • Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 39:10
  • Tidskriftsartikel (refereegranskat)abstract
    • SUMMARY: Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analyses and present analysis results in their histological context. Here, we present semla, an R package for processing, analysis, and visualization of spatially resolved transcriptomics data generated by the Visium platform, that includes interactive web applications for data exploration and tissue annotation. AVAILABILITY AND IMPLEMENTATION: The R package semla is available on GitHub (https://github.com/ludvigla/semla), under the MIT License, and deposited on Zenodo (https://doi.org/10.5281/zenodo.8321645). Documentation and tutorials with detailed descriptions of usage can be found at https://ludvigla.github.io/semla/.
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