{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Junhao Dai"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16003"],"description":["End-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 transit"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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.","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 lengt","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.","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)","Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Junhao Dai"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of primary human mesothelial cells reveals gene expression changes in response to fibrogenic stimulation","description":"End-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 transit","dates":{"release":"2026-09-25T00:00:00Z","modification":"2026-09-25T07:13:26.66Z","creation":"2025-11-06T12:24:42.551Z"},"accession":"E-MTAB-16003","cross_references":{"ENA":["ERP183807"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}