biostudies-arrayexpressJunhao DaiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16003End-stage kidney disease is a growing global health challenge. Kidney replacement options include transplantation, hemodialysis, and peritoneal dialysis, with the latter being the most rapidly expanding and widely accessible form of dialysis worldwide. Notably, peritoneal fibrosis affects approximately half of all peritoneal dialysis patients and leads to multiple modes of treatment failure, driving the need for better mechanistic understanding and novel therapeutic strategies. In this study, we performed an in-depth analysis of the transcriptomic profiles of primary human mesothelial cells under baseline conditions and after fibrogenic stimulation using RNA-seq. Our findings confirm the suppression of branched-chain amino acid catabolism in a TGF-β1-induced mesothelial-mesenchymal transition model, revealing new potential therapeutic avenues for combating peritoneal fibrosis.biostudies-arrayexpressSample Collection - Human primary peritoneal mesothelial cells from independent donors were allocated to Control or TGF-β1 groups (n=4 per group). Cells in the TGF-β1 group were treated with 5 ng/mL TGF-β1 for 12 h before RNA extraction.Sequencing - Sequencing and preprocessing. Indexed libraries were sequenced on Illumina NovaSeq 6000 (paired-end). Raw FASTQ reads were adapter/quality-filtered with fastp (v0.22.0) to produce clean reads. Read mapping and quantification. Clean reads were aligned to the human reference genome with HISAT2 (v2.1.0) using the corresponding GTF annotation. Gene-level counts were obtained with HTSeq (v0.9.1) (exon-based counting). FPKM values were computed for descriptive visualization; all statistical testing used raw counts. Differential expression. Differential analysis used DESeq2 (Bioconductor) with design ~ group. Multiple testing was controlled by Benjamini–Hochberg. Unless otherwise stated, genes were considered differentially expressed at |fold change| > 1.2 (i.e., |log2FC| > log2 1.2) and FDR < 0.05. For interpretation and plotting, positive log2FC indicates higher in Control. Pathway and gene-set analyses. KEGG over-representation was performed with clusterProfiler (organism = hsa). GSEA used fgsea on the genome-wide ranking derived from the DESeq2 Wald statistic (10,000 permutations), reporting NES, FDR and leading-edge genes. Sample-wise activity for the BCAA catabolic core set (BCAT1/2, BCKDHA/B, DBT, DLD, PPM1K, BCKDK, HIBCH, HIBADH, IVD, MCCC1/2) was computed by GSVA/ssGSEA. Visualization. Volcano plots, KEGG dot/bar plots and GSEA running curves were generated in R/ggplot2 with the same thresholds used in the analysis; heatmaps were produced with ComplexHeatmap using per-gene z-scored vst/rlog expression values.Nucleic Acid Extraction - Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.Library Construction - Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). *Read length for mate1(bp)：150bp *Read length for mate2(bp)：150bpSample Treatment - Human primary peritoneal mesothelial cells from independent donors were allocated to Control or TGF-β1 groups (n=4 per group). Cells in the TGF-β1 group were treated with 5 ng/mL TGF-β1 for 12 h before RNA extraction.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Indexed libraries were sequenced on Illumina NovaSeq 6000 (paired-end). Raw FASTQ reads were adapter/quality-filtered with fastp (v0.22.0) to produce clean reads.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensJunhao DaifalseRNA-seq of primary human mesothelial cells reveals gene expression changes in response to fibrogenic stimulationEnd-stage kidney disease is a growing global health challenge. Kidney replacement options include transplantation, hemodialysis, and peritoneal dialysis, with the latter being the most rapidly expanding and widely accessible form of dialysis worldwide. Notably, peritoneal fibrosis affects approximately half of all peritoneal dialysis patients and leads to multiple modes of treatment failure, driving the need for better mechanistic understanding and novel therapeutic strategies. In this study, we performed an in-depth analysis of the transcriptomic profiles of primary human mesothelial cells under baseline conditions and after fibrogenic stimulation using RNA-seq. Our findings confirm the suppression of branched-chain amino acid catabolism in a TGF-β1-induced mesothelial-mesenchymal transition model, revealing new potential therapeutic avenues for combating peritoneal fibrosis.2026-09-25T00:00:00Z2026-09-25T07:13:26.66Z2025-11-06T12:24:42.551ZE-MTAB-16003ERP183807EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969