Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cryptorchidism in the orl rat is associated with muscle patterning defects in the fetal gubernaculum and altered hormonal signaling

ABSTRACT: This study was designed to provide additional insight into testicular hormone production and responsiveness in the orl strain and complement ongoing efforts to characterize the genetic basis of cryptorchidism in this isolated rat colony. Gubernacula were harvested from Long Evans and ORL rat embryos at gestational day 17 and 19. RNA was purified from litter-based organ pools. 26 RNA samples were processed and hybridized to GeneChips. Please note that a mix-up of the samples gubernaculum-GD19-a and -b appears to have occurred as data from these samples clustered with the opposite strain than expected in hierarchical clustering analysis. Thus the strain information was annotated as 'unknown'.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Julia Barthold

PROVIDER: E-GEOD-57924 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Cryptorchidism in the orl rat is associated with muscle patterning defects in the fetal gubernaculum and altered hormonal signaling.

Barthold Julia S JS Robbins Alan A Wang Yanping Y Pugarelli Joan J Mateson Abigail A Anand-Ivell Ravinder R Ivell Richard R McCahan Suzanne M SM Akins Robert E RE

Biology of reproduction 20140625 2

Cryptorchidism, or undescended testis, is a common male genital anomaly of unclear etiology. Hormonal stimulation of the developing fetal gubernaculum by testicular androgens and insulin-like 3 (INSL3) is required for testicular descent. In studies of the orl fetal rat, one of several reported strains with inherited cryptorchidism, we studied hormone levels, gene expression in intact and hormone-stimulated gubernaculum, and imaging of the developing cremaster muscle facilitated by a tissue clear ...[more]

PMID: 24966393

Similar Datasets

Cryptorchidism in the orl rat is associated with muscle patterning defects in the fetal gubernaculum and altered hormonal signaling

Project description:This study was designed to provide additional insight into testicular hormone production and responsiveness in the orl strain and complement ongoing efforts to characterize the genetic basis of cryptorchidism in this isolated rat colony.

2014-07-02 | GSE57924 | GEO

Transcriptional profiling of the rat hypothalamus response to TCDD

Project description:Rodents exposed to the environmental contaminant, TCDD, suffer from a number of acute and chronic toxicities, including lethality and a wasting syndrome. Hypothesizing that the wasting syndrome may be caused by changes in neural control of energy flux and metabolism, we profiled the transcriptional response of rat hypothalamus to TCDD. We employed two separate rat strains: the Long-Evans strain is sensitive to TCDD toxicities while the Han/Wistar strain is over four orders of magnitude more resistant. Surprisingly, few transcriptional changes were induced by TCDD in either strain. Only four genes were altered in Long-Evans rats, including three classic TCDD-responsive genes: Cyp1a1, Cyp1b1, and Nqo1. These three genes were also altered in Han/Wistar rats, along with 133 additional genes. However, the magnitudes of alteration of these additional genes was very modest, with most changes well below two-fold in magnitude. We therefore concluded that rat hypothalamus is mostly refractory to TCDD exposure, at least at the doses and time-points surveyed here.

2009-11-24 | GSE18257 | GEO

Genetic Diversity Influences the Response of the Brain to Developmental Lead Exposure.

Project description:In this study we analyzed the effects of lead-exposure up hippocampal gene expression in males and females exposed to 0ppm, 250ppm and 750ppm lead during two different developmental periods, perinatal (in utero through to weaning at PND21) and postnatal (PND0-PND45), across three strains (Fischer, Long Evans and Sprague Dawley). All tissue was taken at PND 55. We used affymetrix Rat Gene 1.0ST arrays to obtain global gene expression data from each animal, with a group size of 4 for all conditions (Total number of Arrays = 119) Gene expression was profiled in the hippocampus of rats at no lead exposure (0ppm), 250ppm and 750 ppm lead exposure levels during perinatal and postnatal developmental periods of both males and females of three strains of rat (Fischer, Long Evans and Sprague Dawley).

2014-04-10 | E-GEOD-56666 | biostudies-arrayexpress

mRNA Levels in the Rat Liver Display Strain-Specific, Hereditary and AHR-Dependent Components

Project description:Background The rat is a major model organism in toxicogenomics and pharmacogenomics, and the use of steady-state hepatic mRNA levels to predict and understand drug toxicity and mechanism is well-established. Surprisingly, the inter- and intra-strain variability of rat mRNA expression has not been evaluated, nor has the extent of its hereditability been established. We address these issues by studying three rat strains (Long-Evans, Hans/Wistar, and Sprague-Dawley) and two F2 lines derived from Long-Evans x Hans/Wistar crosses. Results Using three independent techniques – variance analysis, linear modelling, and unsupervised pattern recognition – we characterize large amounts of both intra- and inter-strain variability in mRNA levels. Importantly, both sources of variability are highly non-random, and are enriched for specific functional groups. Specific transcription-factor binding-sites are enriched in their promoter regions, and these genes occur in “islands” throughout the rat genome. Using the two F2 crosses we study the hereditability of hepatic mRNA levels and show that the majority of rat genes appear to exhibit directional genetics, with only a small fraction having evidence for interacting loci. Finally, a comparison of inter-strain heterogeneity between mouse and rat orthologs shows more heterogeneity in rats than mice, and find that rat and mouse heterogeneity are uncorrelated. Conclusions Our results establish that hepatic mRNA levels are relatively homogeneous within rat strains, but highly variable between them. This variability may be related to increased activity specific transcription-factors, and has clear functional consequences. Future toxicogenomic and pharmacogenomic studies may take advantage of this phenomenon by surveying panels of rat strains. Keywords: Inter-Strain Comparison

2009-11-24 | GSE10448 | GEO

Transcriptional profiling of the rat hypothalamus response to TCDD

2009-11-23 | E-GEOD-18257 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomics in children with Cryptorchidism

Project description:Cryptorchidism is the most common congenital defect in children's genitourinary system. It is one of the risk factors for male infertility and testicular tumors. The occurrence of cryptorchidism is closely related to many factors, and the alteration of genes plays an important role in the occurrence of cryptorchidism. A large number of studies have confirmed that the formation of cryptorchidism is related to the differential expression of genes. Therefore, exploring new differential expression genes of cryptorchidism from the transcriptome level and studying the relationship between susceptibility genes and children with cryptorchidism can provide a new direction for studying the pathogenesis of cryptorchidism.

2020-04-23 | GSE149084 | GEO

Mating enhances expression of hormonal and trophic factors in the midbrain of female rats

Project description:Among female Long-Evans rats, mating enhances neurosteroid formation in the midbrain ventral tegmental area (independent of peripheral steroid-secreting glands, the ovaries and adrenals). The sources/targets for these actions are not well-understood. In Experiment 1, proestrous rats engaged in a mating paradigm, or did not, and had midbrains assessed via Affymetrix rat genome microarrays. In Experiment 2, the influence of gonadal and adrenal glands on the expression of these genes was assessed in rats that were proestrous, ovariectomized (OVX), or OVX and adrenalectomized (ADX). Microarrays revealed 53 target genes that were significantly up-regulated (> 2.0-fold change) in response to mating. Mating significantly enhanced midbrain mRNA expression of genes involved in hormonal and trophic actions: Gh1, S100g, and Klk1b3 in proestrous, but not OVX and/or ADX, rats; Fshb in all but OVX/ADX rats; and Lhb and Tshb in all rats. Thus, mating enhances midbrain gene expression, independent and dependent of, peripheral glands.

2019-02-28 | GSE127272 | GEO

Transcriptional profiling of the rat adipose tissue response to TCDD

Project description:Rodents exposed to the environmental contaminant, TCDD, suffer from a number of acute and chronic toxicities, including lethality and a wasting syndrome. Hypothesizing that the wasting syndrome may be caused by changes in adipose tissue -- either in its hormonal regulation or in homeostatic effects -- we profiled the transcriptional response of rat white adipose to TCDD. We employed two separate rat strains: the Long-Evans strain is sensitive to TCDD toxicities while the Han/Wistar strain is over four orders of magnitude more resistant. One day after TCDD exposure few genes were altered in either strain, but after four days a modest number of transcriptional alterations were observed. Strikingly, TCDD had far fewer effects than did a feed-restriction protocol intended to mimic the wasting syndrome itself. Notably several classic TCDD-responsive genes were modulated at all time-points, including Cyp1a1, Cyp1b1, and Nqo1. We therefore concluded that rat adipose tissue is unlikely to be the primary driver of the wasting syndrome, and that another tissue is likely involved.

2009-11-24 | GSE18301 | GEO

Transcription profiling of rat liver display strain-specific, hereditary and AHR-Dependent Components

Project description:Background; The rat is a major model organism in toxicogenomics and pharmacogenomics, and the use of steady-state hepatic mRNA levels to predict and understand drug toxicity and mechanism is well-established. Surprisingly, the inter- and intra-strain variability of rat mRNA expression has not been evaluated, nor has the extent of its hereditability been established. We address these issues by studying three rat strains (Long-Evans, Hans/Wistar, and Sprague-Dawley) and two F2 lines derived from Long-Evans x Hans/Wistar crosses. Results; Using three independent techniques â variance analysis, linear modelling, and unsupervised pattern recognition â we characterize large amounts of both intra- and inter-strain variability in mRNA levels. Importantly, both sources of variability are highly non-random, and are enriched for specific functional groups. Specific transcription-factor binding-sites are enriched in their promoter regions, and these genes occur in âislandsâ throughout the rat genome. Using the two F2 crosses we study the hereditability of hepatic mRNA levels and show that the majority of rat genes appear to exhibit directional genetics, with only a small fraction having evidence for interacting loci. Finally, a comparison of inter-strain heterogeneity between mouse and rat orthologs shows more heterogeneity in rats than mice, and find that rat and mouse heterogeneity are uncorrelated. Conclusions; Our results establish that hepatic mRNA levels are relatively homogeneous within rat strains, but highly variable between them. This variability may be related to increased activity specific transcription-factors, and has clear functional consequences. Future toxicogenomic and pharmacogenomic studies may take advantage of this phenomenon by surveying panels of rat strains. Experiment Overall Design: We profiled the basal mRNA levels in three strains and two lines of rat, each using four biological replicates.

2009-11-28 | E-GEOD-10448 | biostudies-arrayexpress

Gene expression in fetal gubernaculum and testis of wildtype (LE/wt) and cryptorchid (LE/orl) rats

Project description:The Long Evans/orl (LE/orl) rat is an animal model of inherited undescended testis (UDT). To explore genetic mechanisms of UDT, we studied differential gene expression in LE/orl and LE wild type (LE/wt) fetal gubernaculum and testis. Analyses of differentially expressed probe sets linked below as supplementary files: Analysis_methods.txt [A description of the analysis] gub.txt [Genes differentially expressed in between wt and orl gubernacula] testes.txt [Genes differentially expressed between wt and orl testes] wt.txt [Genes differentially expressed in wt gubernacular development] Keywords: strain/condition predisposition, disease state analysis, developmental

2008-02-03 | GSE7755 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data