E-PROT-93
Ontology highlight
ABSTRACT:
PROVIDER: E-PROT-93 | ExpressionAtlas | 2022-01-10
REPOSITORIES: ExpressionAtlas
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Project description:Microarrays were used to analyse gene expression underlying early tumourigenesis in Eker rats. Distinct classes of up- and downregulated genes were identified in different preneoplasic lesion vs. microdissected normal (healthy) renal tubules. Laser capture microdissected renal basophilic atypical tubule (bAT) and basophilic atypical hyperplasia (bAH) and healthy tissue (HT) of 6-months aristolochic acid (AA)- and ochratoxin A (OTA)-treated and control (C) male Eker rats were isolated for RNA extraction and microarray analysis in order to investigate gene expression profiles induced by AA and OTA as well as to differentiate pathways specific for the bAT to bAH progression. Keywords: gene expression study, preneoplasic lesion vs. microdissected normal renal tubules
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Project description:Expression data from human with hypertensive nephropathy (HT) We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with HT
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Project description:We obtained gene-expression profiles of microdissected renal-tubule cells from patients with proteinuric nephropathies. Based on the renal function during follow-up, the patients were divided in stable (n=14) and progressive (n=7) subjects (table 1). The cells of interest were laser-capture microdissected from frozen sections from archived kidney biopsy material. Initially all samples were processed as technical duplicates (2 x 21 arrays); due to a large number of signal-negative spots several arrays were excluded leaving 36 arrays for analysis. The samples P2, P6, P7, S10, S13 and S14 were analysed as individual arrays, all other samples were analysed after combination of duplicate arrays. Quality control: To test for reproducibility we calculated the intra-array variability of the duplicate arrays. Duplicate arrays were combined before statistical analysis where applicable. Patient and control characteristics can be found in the manuscript and on our website Frozen kidney biopsies were stained for alkaline phospatase, then the tubule cells were lasercapture microdissected using the PixCell II Laser Capture Microdissection System and CapSure; LCM Caps. Set of arrays that are part of repeated experiments Disease State: samples from patients with proteinuric nephropathy (stable or progressive)
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Project description:Microarrays were used to analyse gene expression underlying early tumourigenesis in Eker rats. Distinct classes of up- and downregulated genes were identified in different preneoplasic lesion vs. microdissected normal (healthy) renal tubules. Laser capture microdissected renal basophilic atypical tubule (bAT) and basophilic atypical hyperplasia (bAH) and healthy tissue (HT) of 6-months aristolochic acid (AA)- and ochratoxin A (OTA)-treated and control (C) male Eker rats were isolated for RNA extraction and microarray analysis in order to investigate gene expression profiles induced by AA and OTA as well as to differentiate pathways specific for the bAT to bAH progression. Keywords: gene expression study, preneoplasic lesion vs. microdissected normal renal tubules For microdissection of preneoplastic lesions from H&E stained renal cryosections, a PALM laser microdissection and pressure catapulting (LMPC) system (PALM Microlaser GmbH) was used. Atypical tubule (bAT), basophilic atypical hyperplasia (bAH) or healthy tissue (HT) were micodissected separately from each of three replicatemale Eker rats per dose group. Lesions of each type or HT from each individual animal were pooled. RNA isolation from pooled samples and subsequent Affymetrix Rat Genome RAE_230A_2.0 chip hybridization was carried out as previously described (Stemmer et al., Toxicology and Applied Pharmacology(2006) Nov 15;217(1):134-42). Time matched controls for microarrays from lesions of OTA and AA treated rats are specified as C(AA) and C(OTA).
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Project description:RNA-seq profiling of microdissected rat renal tubule segments
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Project description:Animal toxins are of interest to a wide range of scientists, due to their numerous applications in pharmacology, neurology, hematology, medicine, and drug research. This, and to a lesser extent the development of new performing tools in transcriptomics and proteomics, has led to an increase in toxin discovery. In this context, providing publicly available data on animal toxins has become essential. The UniProtKB/Swiss-Prot Tox-Prot program (http://www.uniprot.org/program/Toxins) plays a crucial role by providing such an access to venom protein sequences and functions from all venomous species. This program has up to now curated more than 5000 venom proteins to the high-quality standards of UniProtKB/Swiss-Prot (release 2012_02). Proteins targeted by these toxins are also available in the knowledgebase. This paper describes in details the type of information provided by UniProtKB/Swiss-Prot for toxins, as well as the structured format of the knowledgebase.
| S-EPMC3393831 | biostudies-literature
Project description:We obtained gene-expression profiles of microdissected renal-tubule cells from patients with proteinuric nephropathies. Based on the renal function during follow-up, the patients were divided in stable (n=14) and progressive (n=7) subjects (table 1). The cells of interest were laser-capture microdissected from frozen sections from archived kidney biopsy material. Initially all samples were processed as technical duplicates (2 x 21 arrays); due to a large number of signal-negative spots several arrays were excluded leaving 36 arrays for analysis. The samples P2, P6, P7, S10, S13 and S14 were analysed as individual arrays, all other samples were analysed after combination of duplicate arrays. Quality control: To test for reproducibility we calculated the intra-array variability of the duplicate arrays. Duplicate arrays were combined before statistical analysis where applicable. Patient and control characteristics can be found in the manuscript and on our website Frozen kidney biopsies were stained for alkaline phospatase, then the tubule cells were lasercapture microdissected using the PixCell II Laser Capture Microdissection System and CapSure; LCM Caps. Set of arrays that are part of repeated experiments Disease State: samples from patients with proteinuric nephropathy (stable or progressive) Biological Replicate Computed
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Project description:SADE analysis of microdissected kidney
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