Computational protocol: Dual modulation of human hepatic zonation via canonical and non-canonical Wnt pathways

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Protocol publication

[…] RNA-seq data were analyzed with Partek Flow version 4 (Partek). Raw sequencing reads were first trimmed from both ends with a Quality Score method (bases with a quality score of less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nucleotides were excluded from downstream analyses). Trimmed reads were then mapped to the human genome hg38 using Star version 2.4.1d with default parameter settings and Gencode v23 annotation as guidance. Gencode v23 annotation was used to quantify the aligned reads to genes/transcripts using the Partek E/M method. Finally, read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using the Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded). Analysis of variance (ANOVA) False Discovery Rate (FDR)<0.1, FC>2.5 were employed for differential expression analysis. IPA upstream analysis used its default Z score (>2 or <−2) as significant. […]

Pipeline specifications

Software tools Partek Flow, IPA
Application RNA-seq analysis
Organisms Homo sapiens, Rattus norvegicus
Chemicals Oxygen