Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling -- RNA sequencing and Fiji macro scripts

This upload contains the R scripts that were used to perform single-cell RNA sequencing analysis and bulk RNA sequencing analysis and the Fiji script for automated image quantification used in the following article:

Jansen J, van den Berge BT, van den Broek M, Maas RJ, Daviran D, Willemsen B, Roverts R, van der Kruit M, Kuppe C, Reimer KC, Di Giovanni G, Mooren F, Nlandu Q, Mudde H, Wetzels R, den Braanker D, Parr N, Nagai JS, Drenic V, Costa IG, Steenbergen E, Nijenhuis T, Dijkman H, Endlich N, van de Kar NCAJ, Schneider RK, Wetzels JFM, Akiva A, van der Vlag J, Kramann R, Schreuder MF, Smeets B. Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling. Development. 2022 May 1;149(9):dev200198. doi: 10.1242/dev.200198. Epub 2022 May 6. PMID: 35417019; PMCID: PMC9148570.