Filters
Technology
Platform
Mus musculus
35 Downloadable Samples
Illumina HiSeq 2000
Description
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome profiling (RNA-seq) in neuropathic region specific Gaucher mouse brain compared with WT and Isofagamine treated mice of the same age and background and secondly to identify the DEmiRNA associated with the DEmRNA before and after treatment This will give us some insights to see if miRNA is also involved in the the regulation of the expression of the genes involved in the disease process before and after treatment. Methods: 42-45 days old 4L;C*, wild-type (WT) and Isofagamine treated 4L;C* mouse brain were generated by deep sequencing, in triplicate, using IlluminaHiseq. The sequence reads that passed quality filters were analyzed at the gene level with two methods: Burrows–Wheeler Aligner (BWA) followed and TopHat followed by DESeq. qRT–PCR validation was performed using TaqMan and SYBR Green assays Overall design: Regional brain mRNA profiles of ~42 -days old wild type (WT) and 4L;C* an d Isofagamine treated mice were generated by deep sequencing, in triplicate, using IlluminaHi Seq.
Publication Title
Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 26 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Studies using yeast have advanced our understanding of both replicative and chronological aging, leading to the discovery of longevity genes that have homologues in higher eukaryotes. Chronological lifespan in yeast is conventionally defined as the lifespan of a non-dividing cell. To date, this parameter has only been estimated under calorically restricted (CR) conditions, mimicked by starvation. Since post-mitotic cells in higher eukaryotes are rarely calorically-restricted, we sought to develop an alternative experimental system where non-dividing yeast would age chronologically, in the presence of excess nutrients. We report here on a system wherein alginate-encapsulated yeast are packed in a pH- and temperature-controlled bioreactor, then continuously fed non-limiting substrate for extended periods of time. We present demographic, physiological and genomic evidence indicating that after ~120 hrs, immobilized cells cease dividing, remain metabolically very active and retain >95% viability for periods of 17 days. Over the same time interval, starved planktonic cells, cultured using the same media, and also controlled for temperature and pH, retained < 1 % viability in both aerobic and anaerobic cultures,. Unlike planktonic yeast, continuously-fed immobilized cells hyper-accumulate glycogen. FACS analysis of SYTOX green-stained yeast confirms that immobilized cells completely arrest within 5 days of culture, and unlike starving planktonic cells, remain free thereafter of replicative stress and are non-apoptotic. This unusual state is supported by a global gene expression profile that is stable over time, repeatable across replicate experiments, and altogether distinct from planktonic cells cultured in the presence and absence of limiting nutrients. DNA expression profiling, performed here for the very first time on immobilized cells, reveals that glycolytic genes and their trans-acting regulatory elements are upregulated, as are genes involved in remodeling the cell wall and resisting stress; by contrast, many genes that promote cell cycle progression and carry out oxidative metabolism are repressed. Stress resistance transcription factor MSN4 and its upstream effector RIM15 are conspicuously upregulated in the immobilized state, suggesting that nutrient-sensing pathways may play a role in cell viability and longevity when yeast are immobilized and placed in prolonged culture under calorically-unrestricted conditions. The cell cycle arrest in the immobilized state is mediated by RIM 15. Over the time-course of our experiments, well-fed, non-diving immobilized cells do not appear to age.
Publication Title
Uncoupling reproduction from metabolism extends chronological lifespan in yeast.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE84733- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2), Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 12.1.0 (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
An FGFR3/MYC positive feedback loop provides new opportunities for targeted therapies in bladder cancers.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To better understand the molecular mechanisms underlying altered-FGFR3 oncogenic activity in bladder carcinomas, we made use of RT112 cell lines, which were derived from a human bladder tumor and endogenously expressed the FGFR3-TACC3 fusion protein, the growth and transformation of these cell lines being dependent on activated-FGFR3 activity. We conducted a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not with FGFR3 siRNAs.
Publication Title
An FGFR3/MYC positive feedback loop provides new opportunities for targeted therapies in bladder cancers.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Homeobox genes of the Hox class are required for proper patterning of skeletal elements and play a role in cartilage differentiation. In transgenic mice with overexpression of Hoxd4 during cartilage development, we observed severe defects, namely physical instability of cartilage, accumulation of immature chondrocytes, and decreased maturation to hypertrophy. To define the molecular basis underlying these defects, we performed gene expression profiling using the Affymetrix microarray platform.
Publication Title
Microarray Analysis of Defective Cartilage in Hoxc8- and Hoxd4-Transgenic Mice.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Homeobox genes of the Hox class are required for proper patterning of skeletal elements and play a role in cartilage differentiation. In transgenic mice with overexpression of Hoxc8 during cartilage development, we observed severe defects, namely physical instability of cartilage, accumulation of immature chondrocytes, and decreased maturation to hypertrophy. To define the molecular basis underlying these defects, we performed gene expression profiling using the Affymetrix microarray platform.
Publication Title
Microarray Analysis of Defective Cartilage in Hoxc8- and Hoxd4-Transgenic Mice.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 6 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression.
Sample Metadata Fields
Sex, Disease
View Samples- Caenorhabditis elegans
- 6 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Here we exploit the essential process of Xchromosome dosage compensation to elucidate basic mechanisms that control the assembly, genomewide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. The DCC binds to two categories of sites on X: rex sites that recruit the DCC in an autonomous, sequence- dependent manner, and dox sites that reside primarily in promoters of expressed genes and bind the DCC robustly only when attached to X. We find that DCC mutants that abolish rex-site binding do not eliminate dox-site binding, but instead reduce it to the level observed at autosomal binding sites in wild-type animals. Changes in DCC binding to these non-rex sites occur throughout development and correlate with transcriptional activity of adjacent genes. Moreover, autosomal DCC binding is enhanced by rex-site binding in cis in X-autosome fusion chromosomes. Thus, dox and autosomal sites exhibit similar binding properties. Our data support a model for DCC binding in which low-level DCC binding at dox and autosomal sites is dictated by intrinsic properties correlated with high transcriptional activity. Sex-specific DCC recruitment to rex sites then greatly elevates DCC binding to dox sites in cis, which lack intrinsically high DCC affinity on their own. We also show here that the C. elegans DCC achieves dosage compensation through its effects on transcription.
Publication Title
An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Hordeum vulgare
- 44 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Barley cv. Morex inoculated with Fusarium graminearum (isolate Butte 86) or water (mock). Sampled at 24, 48, 72, 96 and 144 hours after treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jayanand Boddu. The equivalent experiment is BB9 at PLEXdb.]
Publication Title
Transcriptome analysis of the barley-Fusarium graminearum interaction.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Analysis of the role of PARP1 in gene transcription in MCF7 cells under non-stress conditions. The hypothesis was that PARP1 activity in MCF7 cells plays a role in gene transcription. The results indicate that PARP1 inhibition does not significantly affect transcription after 6 hours of treatment.
Publication Title
Basal activity of a PARP1-NuA4 complex varies dramatically across cancer cell lines.
Sample Metadata Fields
Specimen part, Cell line
View Samples