Project description:Very little is known about the function of glomerular parietal epithelial cells (PECs). In this study, we performed genome-wide expression analysis on PEC-enriched capsulated vs. PEC-deprived decapsulated rat glomeruli to determine the transcriptional state of PECs under normal conditions. We identified hundreds of differentially expressed genes that mapped to distinct biologic modules including development, tight junction, ion transport, and metabolic processes. Since developmental programs were highly enriched in PECs, we characterized several of their candidate members at the protein level. Collectively, our findings confirm that PECs are multifaceted cells and help define their diverse functional repertoire. We developed a sequential sieving methodology to selectively isolate capsulated (PEC-enriched) glomeruli from un-capsulated (PEC-deprived) glomeruli in rats. Three samples were obtained for each preparation. Total RNA was isolated and its integrity confirmed via Bioanalyzer 2100. Each sample (n =6) was hybridized to an Affymetrix Rat GeneChip 1.0ST microarray.
Project description:In order to understand the kidney compartment specific epigenetic feature of glomeruli, we isolated glomeruli from human kidney biopsy and performed H3K27ac ChIP seq.
Project description:We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection. Collagenase-digested rat renal tubule segments were collected by hand microdissection. Poly(A)-mRNAs were captured from cell lysate and sequenced using paired-end protocol.
Project description:<p>We generated primary cultures from mechanically isolated kidney glomeruli (filtration unit of the nephron) which are composed of podocytes and mesangial cells. In parallel, we generated primary kidney cortex tubule cell cultures, which are composed primarily of proximal tubule cells. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-Seq) and gene expression profiling (RNA-Seq). We found thousands of dynamically regulated enhancers in both cell types that potentially regulate nearby and distal target genes that are differentially expressed. These data will be useful for understanding the epigenomic regulation of gene transcription in key kidney cell types.</p>