Computational protocol: Increased nicotine response in iPSC-derived human neurons carrying the CHRNA5 N398 allele

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Protocol publication

[…] Preparation of cDNA libraries (TruSeq Kit, Illumina) and sequencing (HiSeq 2500, Illumina) were performed by RUCDR Infinite Biologics® (Piscataway, NJ). Data were aligned with human genome using TopHat and analyzed with Cuffdiff and R/BioConductor using the cummeRbund package. Sequencing data can be found in NIH repositories (SRA accession number SRP040275; GEO accession number GSE56398). H1 hESC-derived NSC data for days 0 and 5 are part of GEO series GSE56785. Datasets for DA neuron cultures were from the following SRA accession numbers: SRR1030497, SRR1030496, SRR1030493, and SRR1030492. […]

Pipeline specifications

Software tools TopHat, Cufflinks, CummeRbund
Applications RNA-seq analysis, Transcriptome data visualization
Organisms Homo sapiens
Chemicals Dopamine, Nicotine