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, http://www.qiagen.com) following the manufacturer's recommendations. After cDNA production (manufacturer's protocol; Clontech, Mountain View, CA, http://www.clontech.com) and construction of DNA libraries, the samples were run on an Illumina NextSep500 (Illumina, San Diego, CA, http://www.illumina.com). 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