Computational protocol: Huntington’s Disease Protein Huntingtin Associates with its own mRNA

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Protocol publication

[…] RNA-Seq libraries were made using the SMARTer Ultra Low RNA kit for Illumina (Clontech, Cat # 634935 and 634936), using 1 to 2 ng of RNA. Libraries were run on an Illumina 2500, using a paired end 50 protocol. Sequencing reads were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software. Reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner []. PCR duplicates were removed using the Picard toolkit ( HTSeq package [] was utilized to generate counts for each gene and exon based on number of aligned reads overlapping them. These counts were used to test for differential exon usage using negative binomial generalized linear models and for visualization as implemented by the DEXSeq R package []. […]

Pipeline specifications

Software tools BCL2FASTQ Conversion Software, STAR, Picard, HTSeq, DEXSeq
Application RNA-seq analysis
Organisms Mus musculus
Diseases Huntington Disease, Neurodegenerative Diseases