Project description:Gene expression profiling of CCSK in comparison with non-neoplastic foetal and adult kidney Total RNA extracted from 22 frozen CCSKs and 6 adult non-neoplastic kidneys and comercially obtained RNA from 4 foetal kidneys, were hybridized to Illumina humanHT-12 v4.0 Expression BeadChip at the SCIBLU Lund University Sweden (http://www.lth.se/sciblu).
Project description:The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions. Libraries were prepared using the Illumina TruSeq stranded mRNA protocol and sequenced on the NovaSeq 6000 system at the Center for Translational Genomics (www.ctg.lu.se) in Lund, Sweden. Demultiplexing was performed using the bcl2fastq2 software v2.18.0.12 (Illumina) with default settings and the quality was checked with FastQC v0.11.3. Reads were mapped to the GRCh38 reference genome using the HISAT2 software v2.1.0 and annotation files from release 103. Finally, RNA-sequencing (RNA-seq) expression data in FPKM were calculated with StringTie v1.3.4d.
