biostudies-arrayexpressAntonio RinaldiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15146RNA-sequencing was performed on H1299, HEK293T and CHO-K1 transfected with plasmids expressing EGFP and mKate in an open loop circuit (OL), w/wo compound supplementation, or with iFFL circuit.mKate has target sites for miRNAs highly expressed in the different cell lines (miRNA31 for H1299, miRNA221 for HEK293T and miRNA21 for CHO-K1)biostudies-arrayexpressSample Treatment - Transfections were carried out in 24-well plate for flow cytometry analysis. H1299 cells were transfected with Lipofectamine® 3000 according to manufacturer’s instructions and 300 ng of total DNA in 24-well plates. CHO and HEK293 were transfected with PEI transfection reagent with 300 ng of total DNA in 24-well plates. All cells were plated approximately 24h before transfection at 70000 to 80000 cells per well in 24-wells plates. At the moment of transfection, cells were put in starvation conditions, meaning in poor media for the first 24h. DNA was diluted in Opti-MEM reduced serum media (Gibco), before being mixed and incubated for 25 minutes prior to addition to the cells. All drugs were added 4h after transfection. Modified-RNAs (modRNA) were transfected using Lipofectamine® 3000 protocol under modified conditions in which no P3000 reagent was used. RNA was first diluted in Opti-MEM reduced serum media (Gibco) and it was then mixed with diluted Lipofectamine reagent as manufacturer’s instructions. The mix was incubated for 7 minutes prior to addition to the cells. The fast-forward protocol was used by seeding 120000 cells per well in 24-wells plates at the moment of transfection.Sequencing - Samples were processed with Illumina Novaseq6000Library Construction - Libraries were prepared by Total RNAseq with ribo0 plus (Illumina)OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesData Transformation - Sequence reads were trimmed using bbduk software to remove adapter sequences, poly-A tails and low-quality end bases. Alignment was performed with STAR on the Homo sapiens reference (hg38) provided by UCSC Genome Browser. The expression level of genes was determined with htseq-count using the Gencode/Ensembl gene modelMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensAntonio RinaldifalseTranscriptomic analysis of H1299, HEK293T and CHO-K1 treated with FilgotinibRNA-sequencing was performed on H1299, HEK293T and CHO-K1 transfected with plasmids expressing EGFP and mKate in an open loop circuit (OL), w/wo compound supplementation, or with iFFL circuit.mKate has target sites for miRNAs highly expressed in the different cell lines (miRNA31 for H1299, miRNA221 for HEK293T and miRNA21 for CHO-K1)2025-07-24T00:00:00Z2025-07-24T07:41:28.408Z2025-05-19T09:56:39.516ZE-MTAB-15146ERP172710E-MTAB-14355EFO_0004170EFO_0003816EFO_0003738EFO_0004184EFO_0003969