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Transcription profiling of mammary glands from rats treated with RXR or untreated, to compare results from individual and pooled samples

ABSTRACT: Rat mammary glands were obtained from individual rats in RXR treated (a) and control (b) conditions (12 rats in each condition). The 24 samples were hybridized individually. Also, in each condition, samples were combined into different pools of 2, pools of 3, pools of 12. Technical replicates were also run.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Christina Kendziorski

PROVIDER: E-GEOD-2331 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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On the utility of pooling biological samples in microarray experiments.

Kendziorski C C Irizarry R A RA Chen K-S KS Haag J D JD Gould M N MN

Proceedings of the National Academy of Sciences of the United States of America 20050308 12

Over 15% of the data sets catalogued in the Gene Expression Omnibus Database involve RNA samples that have been pooled before hybridization. Pooling affects data quality and inference, but the exact effects are not yet known because pooling has not been systematically studied in the context of microarray experiments. Here we report on the results of an experiment designed to evaluate the utility of pooling and the impact on identifying differentially expressed genes. We find that inference for m ...[more]

PMID: 15755808

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Rat mammary expression in individuals and pools

Project description:Rat mammary glands were obtained from individual rats in RXR treated (a) and control (b) conditions (12 rats in each condition). The 24 samples were hybridized individually. Also, in each condition, samples were combined into different pools of 2, pools of 3, pools of 12. Technical replicates were also run. Keywords: other

2005-02-25 | GSE2331 | GEO

Rat parathyroid glands LC-MS/MS

Project description:The mechanisms of chronic kidney disease-associated secondary hyperparathyroidism are partially understood. In this project we aimed to gain new information and propose research hypotheses by proteome and phosphoproteome profiling of normal and hyperplastic rat parathyroid glands. Glands were microdissected from rats on normal control diet or CKD-inducing high adenine diet enriched with phosphorus to produce secondary hyperparathyroidism. Protein extracts were pooled from 4 glands (2 rats) for proteome profiling (3 normal and 3 CKD pools), and from 12 glands (6 rats) for phosphoproteome profiling (2 normal and 2 CKD pools).

2022-06-28 | PXD029368 | Pride

Transcriptome profiling of genes regulated by RXR and its partners in monocyte-derived dendritic cells

2010-09-01 | GSE23073 | GEO

Transcriptome profiling of genes regulated by RXR and its partners in monocyte-derived dendritic cells

Project description:CD14+ human monocytes differentiating into DCs in the presence of IL4 and GM-CSF were treated with agonists for RXR and its partners or vehicle 18 hours after plating (experiment with RXR and permissive partners, donor 1-3) or 14 hours after plating (experiment with nonpermissive partners, donor 4-6). Cells were harvested 12 hours thereafter. Experiments were performed in biological triplicates representing samples from three different donors. In this study all probable RXR-signaling pathways induced by agonists for RXR, LXRs, PPARs, RAR and VDR were identified in differentiating human monocyte-derived dendritic cells. In the experiments, differentiating dendritic cells were treated for 12 hours with one of the following compounds (ligands): vehicle (DMS:EtOH 1:1) LG268 (RXR agonist) 9-cis retinoic acid (9cisRA, agonist of RAR and RXR) GW3965 (LXRalpha/beta panagonist) rosiglitazone (RSG, PPARgamma agonist) GW1516 (PPARdelta agonist) AM580 (RARalpha agonist) 1,25-dihydroxyvitamin D3 (VDR agonist)

2010-09-01 | E-GEOD-23073 | biostudies-arrayexpress

RXR mediated neurogenesis (ChIP-Seq)

Project description:A growing number of pieces of evidence suggest the importance of Retinoid X Receptor (RXR)-mediated pathways in neurogenesis and the dysregulation of this signaling in neurodegenerative disorders, such as Alzheimer`s or Amyotrophic Lateral Sclerosis. The data presented here identify the RAR:RXR and LXR:RXR-mediated transcriptional program in embryonic stem cells, neural progenitors and terminally differentiated neurons.

2017-07-22 | GSE101768 | GEO

Expression data from transgenic mice overexpressing RXR-gamma in the skeletal muscle (RXR-gamma mice)

2011-04-08 | GSE28447 | GEO

RXR mediated neurogenesis (RNA-Seq II)

2017-07-18 | GSE101591 | GEO

RXR mediated neurogenesis (RNA-Seq I)

2017-07-18 | GSE101590 | GEO

Expression data from transgenic mice overexpressing RXR-gamma in the skeletal muscle (RXR-gamma mice)

Project description:Retinoid X receptor (RXR)-gamma is a nuclear receptor-type transcription factor expressed mostly in the skeletal muscle, and regulated by nutritional conditions. Previously, we established transgenic mice overexpressing RXR-gamma in the skeletal muscle (RXR-gamma mice), which showed lower blood glucose than the control mice. We used microarrays to investigate their glucose metabolism gene expression change. RNA was isolated from the skeletal muscle of sex- and age-matched RXR-gamma mice and non-transgenic control mice (females at 4 months of age, five samples from each group were combined). Each of the combined samples of the two groups was hybridized to the Affymetrix MG430 microarray.

2011-04-08 | E-GEOD-28447 | biostudies-arrayexpress

Identification of gene expression changes induced by ligands for RXR and its partners in differentiating human monocyte-derived dendritic cells

Project description:Differentiating human dendritic cells were stimulated for 12 hours with RXR agonists (LG268, 9CRA, R- and S-9CDHRA) or agonists for RXR partners including GW3965 (LXRα/β panagonist), RSG (PPARγ agonist), and GW1516 (PPARδ agonist) and AM580 (RARa agonist). The gene expression changes were detected globally by Affymetrix Human Genome U133 Plus 2.0 Arrays.

2015-06-04 | GSE48573 | GEO

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