Transcriptome analysis by RNA-seq technology allows novel insights into gene expression and regulatory networks in health and disease. To better understand the molecular basis of renal fibrosis, we performed RNA-seq analysis in the Unilateral Ureteric Obstruction (UUO) mouse model. We analysed sham operated, 2-and 8-day post-ligation renal tissues. Thousands of genes with statistical significant changes in their expression were identified and classified into cellular processes and molecular pathways. Many novel protein-coding genes were identified, including critical transcription factors with important regulatory roles in other tissues and diseases. Emphasis was placed on long non-coding RNAs (lncRNAs), a class of molecular regulators of multiple and diverse cellular functions. Selected lncRNA genes were further studied and their transcriptional activity was confirmed. For three of them, their transcripts were also examined in other mouse models of nephropathies and their up-or downregulation was found similar to the UUO model. In vitro experiments confirmed that one selected lncRNA is independent of TGFβ or IL1b stimulation but can influence the expression of fibrosis-related proteins and the cellular phenotype. These data provide new information about the involvement of protein-coding and lncRNA genes in nephropathies, which can become novel diagnostic and therapeutic targets in the near future.Chronic kidney disease (CKD) is a frequent condition, causing severe long-term effects with devastating personal and societal consequences 1-3 . There is a need for novel approaches to prevent the decline in renal function during progression of CKD. Considering that the structural basis for this decline is the development of fibrosis, we believe that understanding the molecular basis of renal fibrosis, could offer valuable insights for the improvement of monitoring techniques and therapeutic interventions.To address this question, we combined a systems biology approach in animal models for renal fibrosis, focusing on (but not limited to) the unilateral ureteric obstruction (UUO) model 4,5 . We identified the full transcriptome of renal tissue, using the RNA-seq methodology, during early and late time intervals of kidney fibrosis. This methodology allows the identification of new protein-coding transcripts and novel non-coding RNA transcripts 6 . This is an exciting new direction, since about 75% of the mammalian genome (including human) is transcribed but not translated into proteins, and certain types of non-coding RNAs, especially long non coding RNAs (lncRNAs), play critical regulatory roles in many biological processes 7,8 . However, no data are currently available on the full transcriptome analysis of renal tissue from the UUO model in mice. By performing whole transcriptome sequencing and thorough bioinformatics analysis, we gathered novel information regarding up-regulated and down-regulated genes, pathways and biological processes, and we made lists of differentially expressed genes not suspected so far to be i...