Computational protocol: Peripheral huntingtin silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington’s disease

Similar protocols

Protocol publication

[…] Total RNA was extracted from the hemistriatum as described previously [] for both RNA sequencing (RNAseq) and quantitative reverse-transcription polymerase chain reaction (QRT-PCR). RNAseq was conducted at EA | Q2 Solutions with cDNA libraries prepared using the TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103) for 2x50bp PE sequencing. Quality control, as well as gene and isoform quantification, were performed with an EA | Q2 Solutions developed analysis pipeline, mRNA v7. Bowtie version 0.12.9 was used to align reads to the mouse transcriptome MGSCv37, followed by quantification with RSEM version 1.1.18. RNAseq data are publicly available via the Gene Expression Omnibus (GEO) accession number GSE97101.For QRT-PCR, messenger RNA was reverse transcribed using the Superscript III First Strand Synthesis System (Life Technologies) according to the manufacturer’s protocol. QRT-PCR was conducted and analyzed as described [] using the following taqman probes purchased from Life Technologies: Drd1a: Mm02620146\_s1, N4bp2: Mm01208882\_m1, Islr2: Mm00623260\_s1, Pde10a: Mm00449329\_m1, and β-actin: Mm02619580_g1. All transcripts were normalized to β-actin. […]

Pipeline specifications

Software tools Bowtie, RSEM
Databases GEO
Application RNA-seq analysis
Organisms Mus musculus, Homo sapiens
Diseases Huntington Disease, Peripheral Nervous System Diseases, Heredodegenerative Disorders, Nervous System