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RNASeq of DA neurons from SNpc and VTA

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posted on 2015-03-04, 15:01 authored by William ShinWilliam Shin

RNA-seq of SNpc DA neurons (n=6) and VTA DA neurons (n=6) from Dat bacTRAP mice. Samples are named as "C" for control and "KD" for knockdown. The Fileset contains two files "Parkinson_Validation_VTvsSN_counts.txt", which contains the raw counts after mapping to the mm10, and "Parkinson_Validation_VTvsSN_counts_Normalized.txt", which is the count normalized using DEtransform, a function in the ssMarina package that transforms the data by stabilizing the variance, and adding shot noise. Libraries for RNA sequencing were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, #RS-122-2002), starting the manufacturer’s low-throughput protocol with the end repair step. The concentration of the RNA-Seq libraries was determined on a 2100 Bioanalyzer using High Sensitivity DNA Chips. Subsequently, two libraries with different adapters were multiplexed for sequencing. After confirming the concentration of the multiplexed samples on a 2100 Bioanalyzer using High Sensitivity DNA Chips, samples were analyzed on an Illumina HiSeq 2000 sequencer using 100 bp single-end sequencing.