Computational protocol: Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids

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Protocol publication

[…] hPSCs plated in 2D or 3D were prepared side-by-side using the RNEasy Mini Kit (Qiagen). Samples were subjected to quality control analysis on an Agilent 2100 Bioanalyzer to check for high integrity samples. Qualifying samples were then prepped using the TruSeq stranded mRNA library kit (Illumina). Sequencing was performed on an Illumina NextSeq500 75 × 75 paired end high output run. Samples were aligned to hg19 reference sequence using the TopHat2 splice junction mapper for RNA-Seq reads ( and differential expression calculated using the Cuffdiff program ( […]

Pipeline specifications

Software tools TopHat, Cufflinks
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Amniotic Band Syndrome, Kidney Diseases
Chemicals Methotrexate