Computational protocol: Dataset of TWIST1-regulated genes in the cranial mesoderm and a transcriptome comparison of cranial mesoderm and cranial neural crest

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Protocol publication

[…] Raw microarray data were log2 transformed, quantile normalized and differential expression analyzed using the Linear Models for Microarray (LIMMA, implementation within Gene Pattern. Differentially expressed genes were filtered on a false discovery rate (FDR) of 0.05.For ChIP-Seq data, 50 bp reads were trimmed using Cutadapt , filtered by quality score and aligned to the CanFam3 dog genome using bowtie2 as described . Peaks were called using MACS2 and IDR analysis performed using an IDR cut-off of 0.05. Peak coordinates from two replicates were merged, using the most extreme start and end positions of the two replicates. The equivalent mouse genome (mm10) peak genomic locations were determined using Liftover (NCBI) annotated using the R library ChipSeeker. […]

Pipeline specifications

Software tools limma, cutadapt, Bowtie2, MACS, liftoveR, ChIPseeker
Application ChIP-seq analysis
Organisms Mus musculus