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SRP006435
Mus musculus
2 Downloadable Samples
Illumina Genome Analyzer IIx
Description
The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression levels, and to be able to interpret it mechanistically and functionally. Here we use RNA sequencing of mouse Th2 cells, coupled with a range of other techniques, to show that all genes can be separated, based on their expression abundance, into two distinct groups: one group comprising of lowly expressed and putatively non-functional mRNAs, and the other of highly expressed mRNAs with active chromatin marks at their promoters. Similar observations are made in other data sets, including sources such as Drosophila. Overall design: RNA-seq data of two biological replicates of murine Th2 cells.
Publication Title
Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
During development a specialised subset of endothelial cells, the haemogenic endothelium, undergo an endothelial-to-haematopoietic transition. This process critically involves the transcription factor Runx1. Here we have isolated a specific subpopulation of endothelial cells using a Runx1 enhancer-reporter transgenic mouse line (23GFP). We have compared the gene expression profile of this population to non-23GFP expressing endothelial cells and CD41 expressing haematopoietic progenitor cells to assess whether 23GFP expression marks a biologically distinct subset of endothelium.
Publication Title
Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which cells are plated on a microporous filter whose bottom side only is coated with fibronectin. The cells thus polarize and extend pseudopodial protrusions towards the bottom surface. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter.
Publication Title
Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which serum-starved cells are first plated and allowed to spread on a microporous filter. Addition of LPA at the bottom side of the filter induces the cells to polarize and extend pseudopodial protrusions. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter.
Publication Title
Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
PURPOSE To identify retinal pigment epithelial (RPE)/choroid genes and their relevant expression pathways affected by intravitreal injections of dexamethasone and triamcinolone acetonide in mice at clinically relevant time points for patient care. METHODS Differential gene expression of over 34,000 well-characterized mouse genes, in the RPE/choroid of 6 week old C57BL/6J mice were analyzed after intravitreal steroid injections at 1 week and 1 month post injection, using Affymetrix Mouse Genome 430 2.0 microarrays. The data were analyzed using GeneSpringGX12.5 and Ingenuity Pathway Analysis (IPA) microarray analysis software for biologically relevant changes. RESULTS Both triamcinolone and dexamethasone caused differential activation of genes involved in Circadian Rhythm Signaling pathway at both time points tested. Triamcinolone (TAA) uniquely induced significant changes in gene expression in Calcium Signaling (1 week) and Glutamate Signaling pathways (1month). In contrast, Dexamethasone (Dex) affected the GABA Receptor Signaling (1 week) and Serotonin Receptor Signaling (1month) pathways. CONCLUSIONS Understanding how intraocular steroids affect the gene expression of RPE/choroid is clinically relevant. This in vivo study has elucidated several genes and pathways that are potentially altering the circadian rhythms and several other neurotransmitter pathways in RPE/choroid cells during intravitreal steroid injections, which likely has consequences in the dysregulation of RPE function and neurodegeneration of the retina.
Publication Title
Comparison of In Vivo Gene Expression Profiling of RPE/Choroid following Intravitreal Injection of Dexamethasone and Triamcinolone Acetonide.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To understand the biological pathways involved in twin-twin transfusion syndrome (TTTS) by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA
Publication Title
Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Expression data from xenograft in BALB/c 6-wk-old nude mice with PC3 prostate cancer cells stably expressing PML or a vector control after treatment of the mice with palbociclib (100mg/kg/day diluted in sodium lactate 50mM pH4 given by gavage) during 5 consecutive days
Publication Title
A CDK4/6-Dependent Epigenetic Mechanism Protects Cancer Cells from PML-induced Senescence.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To understand the biological pathways involved in twin-twin transfusion syndrome (TTTS) by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA
Publication Title
Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome.
Sample Metadata Fields
Sex
View Samples