Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic Responses of Laser Capture Microdissected Nephrons from Rat Kidneys Exposed to Single administration of 5 mg/kg Cisplatin : 29 days study - first technical replicate of the RNA sequencing

ABSTRACT: The data contains the transcriptomic responses of the nephron segments (CPT : cortical proximal tubules and PPT : Perimedular proximal tubules) of the rat kidneys exposed to single administration of cisplatin i.v. 5 mg/kg for 29 days (1, 3, 5, 8, 10, 12, 15, 20, 28 days of collection times). The kidneys were fixed with formaldehyde and embedded in paraffin followed by sectioning for 8 um thickness and staining with hematoxylin and eosin staining. The nephron segments were collected using laser capture microdissection microscope for targeted RNA sequencing purposes. The whole kidneys were taken along for the comparison. This RNAseq outcomes suggest different temporal dynamics of transcriptomic responses elicited in different nephron segments upon cisplatin exposure. This RNA-seq outcomes is the first technical replicate of the RNA sequencing. This is part of the TransQST project.

INSTRUMENT(S): Illumina HiSeq 2500, PALM Robo LCM

ORGANISM(S): Rattus norvegicus

SUBMITTER: Lukas Wijaya

PROVIDER: E-MTAB-11969 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Renal excretion of water and major electrolytes exhibits a significant circadian rhythm. This functional periodicity is believed to result, at least in part, from circadian changes in secretion/reabsorption capacities of the distal nephron and collecting ducts. Here, we studied the molecular mechanisms underlying circadian rhythms in the distal nephron segments, i.e. distal convoluted tubule (DCT) and connecting tubule (CNT) and, the cortical collecting duct (CCD). Temporal expression analysis performed on microdissected mouse DCT/CNT or CCD revealed a marked circadian rhythmicity in the expression of a large number of genes crucially involved in various homeostatic functions of the kidney. This analysis also revealed that both DCT/CNT and CCD possess an intrinsic circadian timing system characterized by robust oscillations in the expression of circadian core clock genes (clock, bma11, npas2, per, cry, nr1d1) and clock-controlled Par bZip transcriptional factors dbp, hlf and tef. The clock knockout mice or mice devoid of dbp/hlf/tef (triple knockout) exhibit significant changes in renal expression of several key regulators of water or sodium balance (vasopressin V2 receptor, aquaporin-2, aquaporin-4, M-oM-^AM-!ENaC). Functionally, the loss of clock leads to a complex phenotype characterized by partial diabetes insipidus, dysregulation of sodium excretion rhythms and a significant decrease in blood pressure. Collectively, this study uncovers a major role of molecular clock in renal function. Experiment Overall Design: We examined the temporal profiles of gene expression in mouse distal nephron segments and collecting ducts. The RNA was extracted from microdissected distal convoluted tubules and connecting tubules (DCT/CNT samples) or, cortical collecting ducts (CCD samples). Animals were sacrificed for microdissection every 4 hours, i.e. at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (ZT M-bM-^@M-^S Zeitgeber (circadian) time, indicates time of light-on as ZT0 and time of light-off as ZT12). The microarray hybridization was performed in duplicates on two pools of RNA composed of equivalent amounts of RNA prepared from five animals at each ZT time-point.

Dataset Information

Transcriptomic Responses of Laser Capture Microdissected Nephrons from Rat Kidneys Exposed to Single administration of 5 mg/kg Cisplatin : 29 days study - first technical replicate of the RNA sequencing

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