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rnaseq data processing protocol  (GeneLAB GmbH)

 
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    GeneLAB GmbH rnaseq data processing protocol
    Rnaseq Data Processing Protocol, supplied by GeneLAB GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/rnaseq+data/rnaseq+data+processing+protocol/pmc09576569-234-0-7
    Average 90 stars, based on 1 article reviews
    rnaseq data processing protocol - by Bioz Stars, 2026-11
    90/100 stars

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    Article Title: Muscle atrophy phenotype gene expression during spaceflight is linked to a metabolic crosstalk in both the liver and the muscle in mice
    Article Snippet: Raw FASTQ files were proceed using the “GeneLab RNAseq data processing protocol” as reported at https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-103/ and https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-168 .



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    Co-cultures of GFP2-Display-expressing HIV-1-infected (NLCI JRFL Env) A3.01 cells and GFP1-Display- and CCR5-expressing A3R5.7 target cells were surface-stained for the proteins shown and analyzed by spectral flow cytometry on a Cytek Aurora instrument. Live cells were identified and gated for infection using the mCherry reporter and syncytia were identified as mCherry+GFP+. The values corresponding to each surface protein of interest were normalized to cell size by dividing by the forward scatter height (FSC-H) parameter. (A) UMAP analysis was performed on the resulting datasets, excluding mCherry and GFP so as to not bias the clustering of cell subsets. In other words, the UMAP algorithm was given no information on which cells were uninfected, infected mononucleated, or syncytia. (B) Histograms of each surface protein stained for in the panels, with each cell subset shown as separate overlays. ( C ) Differential gene expression analysis of isolated syncytia VS and isolated infected mononucleated cells. Shown in yellow are genes involved in inflammatory responses and apoptosis. (RNAseq analyses performed by Plasmidsaurus for C ).

    Journal: bioRxiv

    Article Title: HIV-1-induced small T cell syncytia: susceptibility to direct NK cell killing

    doi: 10.64898/2026.06.14.732158

    Figure Lengend Snippet: Co-cultures of GFP2-Display-expressing HIV-1-infected (NLCI JRFL Env) A3.01 cells and GFP1-Display- and CCR5-expressing A3R5.7 target cells were surface-stained for the proteins shown and analyzed by spectral flow cytometry on a Cytek Aurora instrument. Live cells were identified and gated for infection using the mCherry reporter and syncytia were identified as mCherry+GFP+. The values corresponding to each surface protein of interest were normalized to cell size by dividing by the forward scatter height (FSC-H) parameter. (A) UMAP analysis was performed on the resulting datasets, excluding mCherry and GFP so as to not bias the clustering of cell subsets. In other words, the UMAP algorithm was given no information on which cells were uninfected, infected mononucleated, or syncytia. (B) Histograms of each surface protein stained for in the panels, with each cell subset shown as separate overlays. ( C ) Differential gene expression analysis of isolated syncytia VS and isolated infected mononucleated cells. Shown in yellow are genes involved in inflammatory responses and apoptosis. (RNAseq analyses performed by Plasmidsaurus for C ).

    Article Snippet: RNAseq analysis was done by Plasmidsaurus and all RNAseq data figures were generated using their online interface.

    Techniques: Expressing, Infection, Staining, Flow Cytometry, Gene Expression, Isolation, RNA sequencing