Computational protocol: Decreased Expression of CoREST1 and CoREST2 Together with LSD1 and HDAC1/2 during Neuronal Differentiation

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Protocol publication

[…] We used public available RNA-seq data from eight tissues extracted from 3 different rats []. Rat RNA tissue samples were sequenced by an Illumina HiSeq 2000 platform; two rats were sequenced with a 35–50 bp paired-end protocol and one rat was sequenced with a 75–80 bp paired-end protocol. We trimmed the low-quality sequences from the 75–80 bp RNA-seq reads with sickle (available at https://github.com/najoshi/sickle). We used Tophat2 [] to align the reads to the rat reference genome (rn5). The read alignments located at the RCORs loci were assembled with Cufflinks []. To visualize and analyze assembled transcripts we used the UCSC Genome Browser database []. To annotate protein domains at the assembled transcripts, we integrate the rat, mouse and human protein information available at UniProt []. […]

Pipeline specifications

Software tools TopHat, Cufflinks
Databases UCSC Genome Browser
Applications RNA-seq analysis, Genome data visualization
Organisms Rattus norvegicus