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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Exon level expression data from the liver of adult control and Dhx32 homozygous mutant mice

ABSTRACT: We compared the whole mRNA transcript expression from control and homozygous mutant Dhx32 mice by Affymetrix Mouse Exon ST 1.0 Array ST to identify alternatively spliced mRNA transcripts We include exon level expression data from the liver of three control and three Dhx32 homozygous mutant mice 6 total samples (three control and three Dhx32 homozygous mutant) were analyzed. The p values for alternatively spliced transcripts were calculated by using the algorithms of Partek Genomics Suite version 6.4, on core probes excluding probe sets with signals less than 3.

ORGANISM(S): Mus musculus

SUBMITTER: Mohamed Abdelhaleem

PROVIDER: E-GEOD-15133 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Exon level expression data from the liver of adult control and Dhx32 homozygous mutant mice

Project description:We compared the whole mRNA transcript expression from control and homozygous mutant Dhx32 mice by Affymetrix Mouse Exon ST 1.0 Array ST to identify alternatively spliced mRNA transcripts We include exon level expression data from the liver of three control and three Dhx32 homozygous mutant mice

2011-11-17 | GSE15133 | GEO

Exon array analysis in the mouse myoblast cell line, C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA

Project description:CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding in alternative splicing, we performed exon array analysis in C2C12 cells using expression arrays. We analyzed total RNA of C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA. RNA was harvested 48 hrs after transfection.

2012-01-03 | E-GEOD-29990 | biostudies-arrayexpress

The data of differentially regulated exons from mouse testes - wild-type and Dazap1 mutant

Project description:The binding of Deleted in Azoospermia Associated Protein 1 (DAZAP1) to splicing mutations in the BRCA1 and NF1 genes that caused exon exclusion suggest a role for DAZAP1 in RNA splicing. To elucidate the biological functions of DAZAP1 and to search for its natural RNA substrates, we compared the exon usages of wild-type and Dazap1 mutant testes by exon microarrays. We used wild-type and Dazap1 mutant mouse testes. Each genotype has three replicates. 6 total samples were analyzed.

2013-06-01 | E-GEOD-42603 | biostudies-arrayexpress

Alternative splicing is frequent during early embryonic development in mouse

Project description:Background Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of alternative splicing in early embryonic development is based mainly on a few isolated examples. High throughput technologies now allow us to study genome-wide alternative splicing during mouse development. Results A genome-wide analysis of alternative isoform expression in embryonic day 8.5, 9.5 and 11.5 mouse embryos and placenta was carried out using a splicing-sensitive exon microarray. We show that alternative splicing and isoform expression is frequent across developmental stages and tissues, and is comparable in frequency to the variation in whole-transcript expression. The genes that are alternatively spliced across our samples are disproportionately involved in important developmental processes. Finally, we find that a number of RNA binding proteins, including putative splicing factors, are differentially expressed and spliced across our samples suggesting that such proteins may be involved in regulating tissue and temporal variation in isoform expression. Using an example of a well characterized splicing factor, Fox2, we demonstrate that changes in Fox2 expression levels can be used to predict changes in inclusion levels of alternative exons that are flanked by Fox2 binding sites. Conclusions We propose that alternative splicing is an important developmental regulatory mechanism. We further propose that gene expression should routinely be monitored at both the whole transcript and the isoform level in developmental studies. 25 samples were analyzed. Developmental stages e8.5, e9.5 and e11.5 (embryos from all 3, placenta for only e9.5 and e11.5). 5 biological replicates for each.

2010-07-30 | E-GEOD-21971 | biostudies-arrayexpress

Genome wide screening for alternative splicing events in pancreatic cancer

Project description:We used Affymetrix GeneChipM-BM-. Human Exon 1.0 ST Arrays to identify alternative splicing events in 15 samples of PDAC compared to 6 non-tumor samples. Several commercial and open source software approaches for the analysis of differential splicing were tested and a subset of overlapping results was validated using RT-PCR and sequencing. Splicing variants could be validated in several genes closely related to cancer. Pathway analysis of genes predicted to be alternatively spliced revealed an enrichment of genes in categories closely related to cell-cell interactions and kinase activity. 15 samples of pancreatic ductal adenocarcinoma and 6 non tumor pancreatic samples were analyzed for alternative splicing events

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Identification of the altered transcripts in the NMF291–/– cerebellum by exon array.

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2011-10-19 | E-GEOD-33069 | biostudies-arrayexpress

Analysis of RNA from liver tumors in SRSF3 hepatocyte knockout mice

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2015-05-01 | E-GEOD-57019 | biostudies-arrayexpress

Exon Array analysis of WT1(+KTS) mutant mice

Project description:This exon array analysis was performed on mice carrying splice specific mutations at the end of exon9 of the Wilms tumor supressor gene that interfere with the production of WT1(+KTS) isoforms (Hammes et al., 2001; Cell 106:309) 4 wildtype and 4 wt1(+KTS) mutant E18.5 mouse embryos were transcardially perfused with magnetic beads, glomeruli isolated and RNA extracted and analyzed for differential expression on Affymetrix Exon Arrays

2015-03-27 | E-GEOD-67313 | biostudies-arrayexpress

Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations

Project description:The resistance of CML leukemic stem cells (LSC) to tyrosine kinase inhibitor therapies targeting BCR-ABL leads to persistence of disease in most cases. We have identified novel putative therapeutic targets that are differentially expressed in CML LSCs compared to normal hematopoietic stem cells (HSC) by transciptional profiling of stem and progenitor cell populations from CML patients and normal donors. These data are used to obtain 97 genes that are differentially expressed in CML vs. normal stem and progenitor cells and 236 transcripts that show evidence of alternative exon usage in CML vs. normal stem cells. Bone marrow stem and progenitor cell fractions from 5 patients with newly diagnosed and untreated chronic phase CML and 5 healthy donors were analyzed. Contrasts between CML vs. normal stem and progenitors overall and CML vs. normal stem cells were performed using Partek Genomic Suite software. Genes with |log2(fold-change) > 1| and false discovery rate (FDR) of 0.05 were identified as significantly differentially expressed. To identify genes with evidence of alternative exon useage, contrasts between CML and normal stem cell populations were performed, and genes with an alternative splicing FDR of 0.01 were considered to be alternatively spliced.

2013-05-08 | E-GEOD-43754 | biostudies-arrayexpress

Sense and antisense exon profiling across human, mouse, and rat

Project description:Transcription profiling of sense and antisense transcripts of 10 tissues each from human, mouse, and rat. This SuperSeries is composed of the following subset Series: GSE41462: Antisense exon profiling across human, mouse, and rat GSE41464: Sense exon profiling across human, mouse, and rat We profiled the sense and antisense transcription level of 10 tissues each from human, mouse, and rat. Only Affymetrix core probesets were used. Two technical replicates per sample. Reference for protocol: Ge, X., Rubinstein, W.S., Jung, Y.C., and Wu, Q. (2008). Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics 9, 27.

2012-10-10 | E-GEOD-41409 | biostudies-arrayexpress

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