Last updated: 2021-11-24

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Knit directory: amnio-cell-free-RNA/

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Transcriptomic analysis of cell-free RNA from the amniotic fluid of women with suspected cytomegalovirus infection

This site contains the analysis of RNAseq data generated from amniotic fluid cell-free RNA (cfRNA). Amniotic fluid was collected from pregnancies with suspected (and subsequently confirmed by PCR) cytomegalovirus (CMV) infection. Amniotic fluid was also collected from normal pregnancies i.e.  pregnancies that were confirmed by PCR to be negative for CMV infection. Gene expression differences in the cell-free RNA (cfRNA) between the CMV negative and positive pregnancies were identified.

Follow the links below to explore the different parts of the analysis.

Mapping-based DGE analysis

limma-voom

  • DGE analysis (all samples)
    • DGE results: DGE analysis comparing CMV positive and CMV negative samples of the full cohort, using limma.
  • DGE analysis (samples with ultrasound abnormalities excluded)
    • DGE results: DGE analysis comparing CMV positive and CMV negative samples, excluding samples with ultrasound abnormalities, using limma.

RUVseq-edgeR

  • DGE analysis (all samples)
    • DGE results: DGE analysis comparing CMV positive and CMV negative samples of the full cohort, using RUVseq to remove unwanted variation, followed by edgeR.
  • DGE analysis (samples with ultrasound abnormalities excluded)
    • DGE results: DGE analysis comparing CMV positive and CMV negative samples, excluding samples with ultrasound abnormalities, using RUVseq to remove unwanted variation, followed by edgeR.

Mapping-based differential exon usage (DEU) analysis

Licenses

The code in this analysis is covered by the MIT license and the written content on this website is covered by a Creative Commons CC-BY license.

Citations