Characterisation of RESOLUTE parental cell lines

To enable successful SLC function deorphanization we aimed to select minimal number of cell lines covering expression of as many SLCs as possible based on publicly available RNA-Seq dataset of 675 cell lines (Klijn C. et al, Nat. Biotechnol. 2015). A set of 6 adherent human cell lines (HCT116, HuH-7, LS-180, MDA-MB-468, SK-MEL-28, 1321-N1) cumulatively covers expression of about 80 % of all SLCs (TPM  1). These cell lines will be used to generate SLC-knockout and SLC-overexpressing single cell clones. Additionally, Jump In T-REx HEK 293 cells will be used for generating SLC-overexpression cell lines.In order to characterize the transcriptome of the parental cell lines, we performed RNA-Seq on Illumina 4000 with 80 bp single-read setup (Boehringer Ingelheim, Biberach an der Riß, Germany). Quality of sequencing was assessed using FastQC package. After trimming and clipping of Illumina adapter using cutadapt, reads were either mapped to hg38 genome with STAR and then counted in transcript and gene models (ENSEMBL GRCh38 94) with Mix2 (Lexogen), or transcript abundance was quantified with pseudoalignment approach to transcriptome (ENSEMBL GRCh38 94) using kallisto.As the selection of the parental cell lines for RESOLUTE was largely based on original RNA-Seq from Klijn C. et al. we compared newly generated transcriptome profiles with the published data for 5 of the cell lines (HCT116, HuH-7, LS-180, MDA-MB-468, SK-MEL-28). Strong correlation (Pearson correlation coefficient > 0.8) and clustering of cell lines from 2 independent RNA-Seq experiments was observed.In summary, we generated transcriptome profile for 7 cell line which will be used in course of RESOLUTE project. RNA-Seq based transcriptome profile of 1321-N1 and Jump In T-REx HEK 293, to our knowledge, have not been published before. Transcriptome of the RESOLUTE cell lines would be interesting to SLC community as a minimal set of cell lines covering maximal number of expressed SLC (approx. 80%).