Computational protocol: Transcriptomic profiling of human breast and melanoma cells selected by migration through narrow constraints

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Protocol publication

[…] RNA-Sequence analysis and alignment was carried out as described in reference. Quality control checks of raw RNA-Seq data files were done with fastqc v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and fastq_screen v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/). RNA-Seq reads were aligned to the human genome build GRCh38 with TopHat2.0.13 and genome annotation using GRCh38.82.gtf. BAM files were further processed with HTseq0.6.1p1 (http://www.huber.embl.de/users/anders/HTSeq/doc/count.html). Differential analysis of count data was performed by the DESeq2 package (DESeq2). Regularized log transformation was used to transform the DESeq2 data for principal component analysis. […]

Pipeline specifications

Software tools FastQC, FastQ Screen, TopHat, HTSeq, DESeq2
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Breast Neoplasms, Melanoma, Neoplasms