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Transcription profiling of rat Adamts16 variants linked to inherited hypertension: knockdown of Adamts16 in NRK-52E cells

ABSTRACT: We used Affymetrix GeneChips to expression profile rat kidney NRK-52E cells treated with control scrambled siRNA or siRNA specifically targeting Adamts16. The goal of this project was to identify the downstream genes regulated by Adamts16 (the function of Adamts16 has yet to be fully delineated). Gene expression differences resulting from these siRNA-mediated gene knockdown experiments will be compared to the gene expression profiling experiments comparing kidneys from Dahl salt-senstive hypertensive inbred strain versus less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain. The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. Gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S are hypothesized to result from sequence differences between the S and LEWIS alleles for Adamts16. It is further hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. The downstream genes regulated by Adamts16 may provide insight pertaining to the mechanism of blood pressure differences. Experiment Overall Design: RNA from 3 independent cultures of NRK-52E cells treated with scrambled control siRNA was extracted for target preparation and hybridization onto Affymetrix GeneChips. We also isolated RNA from NRK-52E cells treated with two different siRNAs targeting Adamts16 (n=2 independent cultures for each siRNA) for target preparation and hybridization onto Affymetrix GeneChips.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Norman Lee

PROVIDER: E-GEOD-12724 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Positional identification of Adamts16 variants linked to inherited hypertension: gene expression of congenic vs S rats

Project description:We used Affymetrix GeneChips to expression profile kidneys from Dahl salt-senstive hypertensive inbred strain and less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain to identify genes downstream of Adamts16 (the function of Adamts16 has yet to be fully delineated). The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. It is hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. We further hypothesize that gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S result from sequence differences between the S and LEWIS alleles of Adamts16. Lastly, the downstream genes differentially regulated by the Adamts16 alleles may provide insight pertaining to the mechanism of blood pressure differences. Gene expression differences resulting from these kidney comparisons will be compared to the gene expression profiling experiments comparing siRNA-mediated knockdown of Adamts16 in NRK-52E kidney cells versus scrambled siRNA control. Keywords: Genetic modification, disease state analysis

2008-11-01 | GSE12725 | GEO

Positional identification of Adamts16 variants linked to inherited hypertension: knockdown of Adamts16 in NRK-52E cells

Project description:We used Affymetrix GeneChips to expression profile rat kidney NRK-52E cells treated with control scrambled siRNA or siRNA specifically targeting Adamts16. The goal of this project was to identify the downstream genes regulated by Adamts16 (the function of Adamts16 has yet to be fully delineated). Gene expression differences resulting from these siRNA-mediated gene knockdown experiments will be compared to the gene expression profiling experiments comparing kidneys from Dahl salt-senstive hypertensive inbred strain versus less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain. The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. Gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S are hypothesized to result from sequence differences between the S and LEWIS alleles for Adamts16. It is further hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. The downstream genes regulated by Adamts16 may provide insight pertaining to the mechanism of blood pressure differences. Keywords: Gene knockdown with siRNA

2008-11-01 | GSE12724 | GEO

Transcription profiling of rat Adamts16 variants linked to inherited hypertension: gene expression of congenic vs S rats

Project description:We used Affymetrix GeneChips to expression profile kidneys from Dahl salt-senstive hypertensive inbred strain and less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain to identify genes downstream of Adamts16 (the function of Adamts16 has yet to be fully delineated). The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. It is hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. We further hypothesize that gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S result from sequence differences between the S and LEWIS alleles of Adamts16. Lastly, the downstream genes differentially regulated by the Adamts16 alleles may provide insight pertaining to the mechanism of blood pressure differences. Gene expression differences resulting from these kidney comparisons will be compared to the gene expression profiling experiments comparing siRNA-mediated knockdown of Adamts16 in NRK-52E kidney cells versus scrambled siRNA control. Experiment Overall Design: Kidney RNA from 3 Dahl salt-sensitive rats was extracted for target preparation and hybridization onto Affymetrix GeneChips. We also isolated kidney RNA from 3 S.LEW(D1MCO4x1x3Bx1) congenic rats for target preparation and hybridization onto Affymetrix GeneChips.

2008-11-13 | E-GEOD-12725 | biostudies-arrayexpress

Expression data from EMT-derived NRK-52E cells before and after the AMPKα2 knockdown

Project description:Recent studies have shown that AMPKα2 can regulate epithelial-mesenchymal transition(EMT) processes during kidney fibrosis. However, the underlying mechanisms for AMPKα2 changes in renal tubular EMT remain unclear. TGF-β1 was used to induce epithelial-mesenchymal transition(EMT) in normal rat renal tubular epithelial (NRK-52E) cells. Gene microarray was used to analyze differential gene expression in EMT-derived NRK-52E cells before and after the AMPKα2 knockout

2019-12-18 | GSE141981 | GEO

Expression data from NRK-52E cells treated with aristolochic acids for 6h, 24h and 72h

Project description:In this study we have examined the effect of sub-cytotoxic exposure to aristolochic acids (1.65µM) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E). We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of aristolochic acids in rat renal proximal cells. NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to aristolochic acid dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.65 ?M) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.

2015-07-02 | E-GEOD-68687 | biostudies-arrayexpress

Acidosis activates the Nrf2-pathway in renal proximal tubule-derived cells through a crosstalk with renal fibroblasts

Project description:Crosstalk of renal epithelial cells with interstitial fibroblasts plays an important role in kidney pathophysiology. A former study showed that crosstalk between renal epithelial cells and renal fibroblasts protects against acidosis-induced damage. In order to gain further mechanistic insight into this crosstalk we investigated the effect of acidosis on the transcriptome of renal epithelial cells (NRK-52E) and renal fibroblasts (NRK-49F) in co-culture by RNASeq, bioinformatics analysis and experimental validation.

2023-02-27 | GSE218626 | GEO

Identification of molecules from dying cells that act as signals to promote proliferation of surrounding cells

Project description:To elucidate the mechanisms underlying epithelial homeostasis, we explored molecules that might serve as M-bM-^@M-^\dangerM-bM-^@M-^] signals in mediating epithelial regeneration with microarray. We hypothesize that soluble factors may have been released from damaged cells to stimulate the proliferation of surviving epithelial cells. In elucidating the mechanism of dying cell-to-surviving cell communication using normal rat kidney NRK-52E epithelial cells, we observed gene expression profiles in these cells after the induction of cell death using hydrogen peroxide. The results demonstrated up-regulation of Interleukin-6, Heme oxygenase-1 and Hypoxia inducible factor-1 alpha in dying cells. Global gene expression changes were measured after induction of cell death in NRK-52E cells after incubation with hydrogen peroxide. Hydrogen peroxide (0, 0.003, 0.006, 0.009% in DMEM) was teated for 1 hour. After wash with PBS, cells were incubated with non-serum DMEM for 12 hours.

2015-01-08 | E-GEOD-64733 | biostudies-arrayexpress

Expression data from HeLa cells after hnRNP L knockdown (versus luciferase control), including cycloheximide treatment

Project description:Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD. Supplementary files GSE37561_activated_exon.txt and GSE37561_repressed_exon.txt list exons predicted to be activated and repressed by hnRNPL, respectively. 3 biological replicates of hnRNP L (luciferase) knockdown samples

2014-02-13 | E-GEOD-37561 | biostudies-arrayexpress

Rattus norvegicus

Project description:NRK-52E cells transcriptomes raw sequence reads

| PRJNA842539 | ENA

Transcription poisoning by topoisomerase I is controlled by gene length, splice sites and miR-142-3p

Project description:DNA topoisomerase I (Top1) is required for transcription as it relaxes positive and negative supercoils by forming transient Top1 cleavage complexes (Top1cc) up- and down-stream of transcription complexes. However, Top1cc can also be trapped by endogenous DNA lesions and by camptothecin (CPT) and its anticancer derivatives, which results in transcription blocks. Here, we undertook a genome-wide analysis of the effects of CPT on gene expression at exon resolution. We tested the impact of Top1 inhibition on gene expression at the genome-wide level in human colon carcinoma HCT116 and human breast carcinoma MCF7 cells. The RNA of cells treated with camptothecin (CPT) for various times was analyzed with Affy Exon array (GeneChip Human Exon 1.0 ST array). Moreover, we tested the impact of Top1 down-regulation on gene expression at the genome-wide level in human colon carcinoma HCT116 cells. The RNA of cells treated transfected with a Top1 siRNA was analyzed with Affy Exon array (GeneChip Human Exon 1.0 ST array).

2013-04-17 | E-GEOD-37352 | biostudies-arrayexpress

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