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GSE11915
Homo sapiens
24 Downloadable Samples
Illumina human-6 v2.0 expression beadchip, Affymetrix Human Genome U133A Array (hgu133a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
SOX4 is a critical developmental transcription factor in vertebrates and is required for precise differentiation and proliferation in multiple tissues. In addition, SOX4 is overexpressed in many human malignancies, but the precise role of SOX4 in cancer progression is not well understood. Here we have performed an expression profiling experiment of LNCaP cells either overexpressing SOX4 or GFP to identify SOX4 target genes.
Publication Title
Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
SOX4 is a critical developmental transcription factor in vertebrates and is required for precise differentiation and proliferation in multiple tissues. In addition, SOX4 is overexpressed in many human malignancies, but the precise role of SOX4 in cancer progression is not well understood. Here we have either eliminated SOX4 using siRNA or overexpressed a SOX4 cDNA and compared the gene expression patterns against control GFP transfections to identify SOX4 target genes.
Publication Title
Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 24 Downloadable Samples
Illumina HiSeq 4000
Description
Purpose: identifying genes responding to insulin stimulation in S2R+ cells through whole transcriptome RNA-seq analyses Methods: Total RNA was extracted from S2R+ cells using TRIzol® reagent (Invitrogen). After assessing RNA quality with an Agilent Bioanalyzer, libraries were constructed with Illumina TruSeq mRNA Library Prep Kit , libraries were sequenced using an Illumina HiSeq 4000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). Results: Using an time series data analysis workflow incorporating polynormials , we identified 1254 temproally differentially expressed genes responding to insulin stimulation in the S2R+ cells. Overall design: the pre-starved S2R+ cells ( with serum free medium) were stimulated with insulin; triplicate samples were collected at basline and every 20minutes time interval up to three hours; transcriptome profiling
Publication Title
Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells.
Sample Metadata Fields
Specimen part, Treatment, Subject, Time
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Identification of genes involved in ocular birth defects remains a challenge. To facilitate the identification of genes associated with cataract, we developed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE contains microarray gene expression profiles of the mouse embryonic lens as it transitions from the stage of placode invagination to that of vesicle formation. We identified differentially regulated genes by comparing lens microarray profiles to those representing whole embryonic body (WB) without ocular tissue. These were then utilized to generate a ranked list of lens-genes enrichment, which can be viewed as iSyTE tracks in the UCSC Genome browser to aid identification of genes with lens function.
Publication Title
iSyTE: integrated Systems Tool for Eye gene discovery.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 6 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
The hlh-30 gene encodes a C. elegans basic-helix-loop-helix (bHLH) transcription factor; We compared RNA from wild type worms and worms mutant for the hlh-30 gene to identify putative target genes of the HLH-30 transcription factor.
Publication Title
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Background: Skin aging is associated with intrinsic processes that compromise structure of the extracellular matrix while promoting loss of functional and regenerative capacity. These processes are accompanied by a large-scale shift in gene expression, but underlying mechanisms are not understood and conservation of these mechanisms between humans and mice is uncertain. Results: We used genome-wide expression profiling to investigate the aging skin transcriptome. In humans, age-related shifts in gene expression were sex-specific. In females, aging increased expression of transcripts associated with T-cells, B-cells and dendritic cells, and decreased expression of genes in regions with elevated Zeb1, AP-2 and YY1 motif density. In males, however, these effects were contrasting or absent. When age-associated gene expression patterns in human skin were compared to those in tail skin from CB6F1 mice, overall human-mouse correspondence was weak. Moreover, inflammatory gene expression patterns were not induced with aging of mouse tail skin, and well-known aging biomarkers were in fact decreased (e.g., Clec7a, Lyz1 and Lyz2). These unexpected patterns and weak human-mouse correspondence may be due to decreased abundance of antigen presenting cells in mouse tail skin with age. Conclusions: Aging is generally associated with a pro-inflammatory state, but we have identified an exception to this pattern with aging of CB6F1 mouse tail skin. Aging therefore does not uniformly heighten inflammatory status across all mouse tissues. Furthermore, we identified both intercellular and intracellular mechanisms of transcriptome aging, including those that are sex- and species-specific.
Publication Title
Meta-profiles of gene expression during aging: limited similarities between mouse and human and an unexpectedly decreased inflammatory signature.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 15 Downloadable Samples
- NextSeq500
Description
Nkx2.2, Nkx6.1, and Olig2 repressors were overexpressed, singly or in combination, in in vitro-derived mouse neural progenitors to identify thier repression targets Overall design: Overexpression study to identify genes repressed by Nkx2.2, Nkx6.1, and Olig2 in neural progenitors
Publication Title
A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer
Description
Tbx20 is a transcription factor important for heart development. To assess the role of Tbx20 in the adult heart, we generated a conditional knockout for this gene, specifically in cardiomyocytes. We profiled gene expression levels using RNA-seq in both normal and knockout adult mouse hearts to identify genes and pathways regulated by Tbx20. The article describing the Tbx20 knockout mouse is under review, a reference will be added when published. Overall design: Analysis of triplicate mRNA samples of adult mouse, comparing normal and knockout
Publication Title
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 11 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Homeodomain (HD) proteins comprise a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, yet they paradoxically recognize very similar DNA sequences. To investigate how HDs control cell-specific gene expression patterns, we determined the DNA binding specificities of a broad range of HDs critical for Drosophila embryonic mesoderm development. These studies revealed particular sequences that are bound by one HD and not by others. Such HD-preferred binding sites are overrepresented in the noncoding regions of genes that are regulated by the corresponding HD. Moreover, we show at single-cell resolution in intact embryos that the HD Slouch (Slou) controls myoblast gene expression through unique DNA sequences that are preferentially bound by Slou. These findings demonstrate that the sequence of a HD-binding site dictates which HD family member binds to and regulates a particular enhancer. This represents a novel mechanism for how cell type-specific TFs induce the distinct genetic programs of individual embryonic cells.
Publication Title
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.
Sample Metadata Fields
Specimen part
View Samples