Computational protocol: Direct Isolation and Characterization of Human Nephron Progenitors

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Protocol publication

[…] RNA extraction was performed immediately after FACS (passage 0) using the RNeasy Micro Kit (Qiagen, Valencia, CA, following the manufacturer's recommendations. After cDNA production (manufacturer's protocol; Clontech, Mountain View, CA, and construction of DNA libraries, the samples were run on an Illumina NextSep500 (Illumina, San Diego, CA, Differential gene expression was analyzed using ERCC ExFold probes with the Remove Unwanted Variation R/Bioconductor software package combined with edgeR . Gene ontology enrichment analysis was performed using GOstats R/Bioconductor software . A detailed description of the RNA‐seq method and data analysis is provided in the supplemental online data. Data have been deposited in Gene Expression Omnibus (GEO) under accession number GEO: GSE74450. […]

Pipeline specifications

Software tools edgeR, GOstats
Databases GEO
Application RNA-seq analysis
Organisms Homo sapiens, Mus musculus