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SRP125980
Mus musculus
12 Downloadable Samples
Illumina HiSeq 2500
Description
RNA was isolated from FFPE samples of IDH1 mutant, WT tumors and normal brains Overall design: Determination of the glioma subtype in IDH1 mutant and WT tumors
Publication Title
Mutant IDH1 Promotes Glioma Formation In Vivo.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 14 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The undifferentiated state of pluripotent stem cells depends heavily on the culture conditions. We show that a unique combination of small molecules, SMC4, added to culture conditions converts primed pluripotent stem cells to a more nave state. By conducting Affymetix analysis we show of majority of lineage markers are repressed in SMC4 culture.
Publication Title
A novel platform to enable the high-throughput derivation and characterization of feeder-free human iPSCs.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Genome-wide gene expression analysis of MyoD-infected DMD-specific iPSCs (GM05112-M5.1) on days 0 (untreated), day 3 and day 8 post Dox treatment, human primary myoblasts (undifferentiated and as differentiated myotubes), and undifferentiated iPSCs from healthy donors (iPSCs-1 and iPSCs-2).
Publication Title
Myogenic differentiation of muscular dystrophy-specific induced pluripotent stem cells for use in drug discovery.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
- Illumina HiSeq 2000
Description
To dissect regulatory processes of cell proliferation and differentiation we generated mouse strains carrying any combination of the four Stat5 alleles, thus expressing STAT5 from 0 to 100%. RNA-Seq analyses revealed that different STAT5 levels activate specific genetic programs linked to cell proliferation and differentiation. Overall design: We refer to wild-type mice and Stat5abfl/fl mice as AABB mice; Stat5abfl/fl;MMTV-Cre (with Stat5ab-deficient mammary epithelial cells) as Null mice; Stat5a-/- mice as BB mice; Stat5b-/- mice as AA mice; Stat5ab+/null mice as AB mice.
Publication Title
Sequential activation of genetic programs in mouse mammary epithelium during pregnancy depends on STAT5A/B concentration.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Background: Several genetic defects of the nucleotide excision repair (NER) pathway, including deficiency of the Excision Repair Cross-Complementing rodent repair deficiency, complementation group 1 (ERCC1), result in pre-mature aging, impaired growth, microcephaly and delayed development of the cerebellum. Such a phenotype also occurs in ERCC1-knockout mice which survive for up to 4 weeks after birth. Therefore, we analyzed cerebellar and hippocamapal transcriptomes of these animals at 3 weeks of age to identify the candidate mechanisms underlying brain consequences of reduced ERCC1 activity.
Publication Title
Downregulation of cholesterol biosynthesis genes in the forebrain of ERCC1-deficient mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF-family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium using tissue-specific, inducible beta-catenin gene ablation in adult mice. Block of Wnt/beta-catenin signaling resulted in rapid loss of transient-amplifying cells and crypt structures. Importantly, intestinal stem cells were induced to terminally differentiate upon deletion of beta-catenin resulting in a complete block of intestinal homeostasis and fatal loss of intestinal function. Transcriptional profiling of mutant crypt mRNA isolated by laser capture micro dissection confirmed those observations and allowed to identify genes potentially responsible for the functional preservation of intestinal stem cells.
Publication Title
Wnt/beta-catenin is essential for intestinal homeostasis and maintenance of intestinal stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human pluripotent stem cells in culture are often associated with the prime state which represents a more developed state relative to the nave state which is often associated with the inner cell mass and thought to have the potential to give rise to all cell types. We have developed a small molecule-driven cocktail FMM that maintains human pluripotent stem cells in a state similar to the naive state as defined by several properties including gene expression profile.
Publication Title
Platform for induction and maintenance of transgene-free hiPSCs resembling ground state pluripotent stem cells.
Sample Metadata Fields
Specimen part
View Samples- Vitis vinifera
- 174 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 48 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Preeclampsia (PE) is a complex, heterogeneous disorder of pregnancy, demonstrating considerable variability in observed maternal symptoms and fetal outcomes. We recently identified five clusters of placentas within a large gene expression microarray dataset (N=330, GSE75010), of which four contained a substantial number of PE samples. However, while transcriptional analysis of placentas can subtype patients, we hypothesized that the addition of epigenetic information should reveal gene regulatory mechanisms behind the distinct PE pathologies. We, therefore, subjected 48 of our samples to Infinium Human Methylation 450K arrays and investigated relationships between the gene expression and DNA methylation data.
Publication Title
Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Homo sapiens
- 65 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Splenic marginal zone lymphoma (SMZL) is a rare, indolent non-Hodgkin’s lymphoma that affects 0.13 per 100,000 persons annually. Overall survival of SMZL is estimated to reach 8 to 11 years in most cases, but up to 30% of SMZL cases develop aggressive presentations resulting in greatly diminished time of survival. SMZL presents with a very heterogeneous molecular profile, making diagnosis problematic and accurate prognosis even less likely. The study herein has utilized this data to assist in identifying a potential diagnostic gene expression signature with highly specific predictive utility for further evaluation among control and SMZL patient samples. Delineation of a unique SMZL signature that could provide diagnostic utility for a malignancy that has historically been difficult to identify. These results should be further investigated and validated in subsequent molecular investigations of SMZL so it may be potentially incorporated into standard oncology practice for improving the understanding and outlook for SMZL patients.
Publication Title
Identification of a Splenic Marginal Zone Lymphoma Signature: Preliminary Findings With Diagnostic Potential.
Sample Metadata Fields
No sample metadata fields
View Samples