Global RNA-seq for a RNA targeted small molecule that triggers elimination of r(G4C2)exp in c9ALS/FTD
This is a supplemental dataset for a manuscript studying a a RNA targeted small molecule that triggers elimination of r(G4C2)exp in c9ALS/FTD. The effect of the small molecule on the human transcriptome was analyzed by RNA-seq in both iPSCs from the patient and the healthy donor.
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Total RNA integrity was confirmed by Agilent 2100 Bioanalyzer RNA nano chip, and the quantity was measured by Qubit 2.0 Fluorometer (Invitrogen). The library preparation was performed using NEBNext Ultra II Directional RNA kit (NEB, E7760) in combination with NEBNext rRNA depletion module (NEB, E6310) and RNA fragmentation module (NEB, E6150S), following manufacture’s recommendations. Briefly, a total of 200 ng RNA was first processed with depleted of ribosomal RNA, and then randomly fragmented to achieve range between 150 to 300 nucleotides. The fragmented RNAs were random primed for the first-strand synthesis, and the second strand was synthesized with dUTPs. The strand information is thus preserved by using USER enzyme (Uracil-specific excision reagent). The cDNA was PCR amplified and pooled equimolar to load onto the NextSeq 500 v2.5 flow cell and sequenced with 2 x 40bp paired-end method. The output fastq files were aligned using STAR. The read counts of specific regions were extracted using samtools. The global differential gene expression analysis was performed using featureCounts and Deseq2.