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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- 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- 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- Vitis vinifera
- 38 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Changes in gene expression during berry development during a grape growing season were analysed.
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- Caenorhabditis elegans
- 12 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Analysis of gene expression in worms exposed to PA14 for 4 hours. Worms used were wild-type or fshr-1(ok778) mutants. Comparisons allowed determination of fshr-1-dependent gene expression.
Publication Title
The Conserved G-Protein Coupled Receptor FSHR-1 Regulates Protective Host Responses to Infection and Oxidative Stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
In order to identify genes with different overall transcript levels or differential exon levels (alternative processing) between the groups Control and Tat-SF1KD, we studied 11 hybridizations on the HumanExon10ST array using mixed model analysis of variance. 526 genes with significant transcript level differences between the groups and 1397 genes with significant differential exon levels were found, including 99 genes with both transcript and exon level differences (p<0.01).
Publication Title
Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.
Sample Metadata Fields
Cell line
View Samples