TechNOA™ - Predesigned Antisense Oligonucleotides for Splice Modulation

Gene expression data is downloaded from the VastDB resource. There are 108 human RNA-seq datasets in this resource.

cRPKM: corrected Reads Per Kilobase per Million mapped reads. Correction is done by discounting transcript effective length if reads are mapped to multiple locations in the transcriptome (Labbe et al 2012).

The suffixes "_a, _b, _c, _d" etc. represent pools of multiple individual RNA-seq experiments from comparable tissues or cell types to increase the read depth. Click here for a complete mapping to their sample data sources.

Labbe RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ. 2012. A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells 30: 1734-1745.

Gene expression data is downloaded from the CCLE/DepMap, Broad (2020): DepMap 20Q2 Public resource. CCLE performed RNA sequencing on 1,019 cell lines (Mahmou Ghandi et al 2019).

TPM: transcripts per million. Gene expression data is normalized using RSEM (Li & Dewey 2011). TPM values were log2 transformed to prevent correlation values from being dominated by the most abundant transcripts and a pseudo-count of 1 is added to all transcripts prior to transformation to avoid computational error or a very large negative number in log2 transform when the expression value is very small.

Cell Line: Click here for more information on the cell lines.

Mahmou Ghandi et al. 2019. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569: 503–508.
Bo Li, Colin Dewey 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.

Transcript expression data is downloaded from the CCLE/DepMap, Broad (2020): DepMap 20Q2 Public resource. CCLE performed RNA sequencing on 1,019 cell lines (Mahmou Ghandi et al 2019).

Count: RNAseq transcript count data using RSEM. CCLE expression data is quantified from RNAseq files using the GTEx pipelines.

Cell Line: Click here for more information on the cell lines.

Mahmou Ghandi et al. 2019. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569: 503–508.
Bo Li, Colin Dewey 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.

SpliceMod™

Transcript Expression - CCLE