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GSE85921
Homo sapiens
8 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip, Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
<i>APOL1</i> Renal-Risk Variants Induce Mitochondrial Dysfunction.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20), Illumina HumanHT-12 V4.0 expression beadchip
Description
To assess differential gene expression by APOL1 renal-risk (2 risk alleles) vs. non-risk (G0G0) genotypes in primary proximal tubule cells (PTCs), global gene expression (mRNA) levels were examined on Affymetrix HTA 2.0 arrays in primary PTCs cultured from non-diseased kidney in African Americans without CKD who underwent nephrectomy for localized renal cell carcinoma.
Publication Title
<i>APOL1</i> Renal-Risk Variants Induce Mitochondrial Dysfunction.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 1 Downloadable Sample
- Affymetrix Human Transcriptome Array 2.0 (hta20), Illumina HumanHT-12 V4.0 expression beadchip
Description
To elucidate pathways whereby apolipoprotein L1 gene (APOL1) G1 and G2 variants facilitate kidney disease in African Americans, human embryonic kidney cells (HEK293) were used to establish doxycycline-inducible (Tet-on) cell lines stably expressing reference APOL1 G0 and its G1 and G2 renal-risk variants. Illumina human HT-12-v4 arrays and Affymetrix HTA 2.0 arrays were employed to generate global gene expression data with doxycycline induction. Significantly altered pathways identified through bioinformatics involved mitochondrial function; results were validated using immunoblotting, immunofluorescence and functional assays.
Publication Title
<i>APOL1</i> Renal-Risk Variants Induce Mitochondrial Dysfunction.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 11 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Genome wide mRNA and miRNA profiling was performed in SH-SY5Y cells stably overexpressing wild type or mutant MIR204 or MIR618. Mutants came from a large scale genetic screening of brain expressed miRNA genes in patients with schizophrenia or idiopathic generalized epilepsy and in control individuals. Based on enrichment of the variants with the schizophrenic or epileptic phenotype and based on impact prediction, two variants, one near MIR204 (rs7861254) and one in MIR618 (rs2682818) were selected for functional validation. Genome wide profiling of mRNA (micro-array) and mature miRNAs (small RNA sequencing, submitted to SRA) was performed in the created stable cells to assess the effect of the variants and to investigate the function of these miRNA genes.
Publication Title
Schizophrenia-Associated MIR204 Regulates Noncoding RNAs and Affects Neurotransmitter and Ion Channel Gene Sets.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
Illumina Genome Analyzer IIx
Description
3 weeks old aseptically grown WT and loss-of-function lines of SnRK1s (transgenic SnRK1a1 T-DNA insertion mutant line crossed with an estradiol inducible amiRNA construct targeting SnRK1a2) and group S1 bZIPs (bZIP1/bZIP53 T-DNA insertion mutant line crossed with an estradiol inducible amiRNA construct simultaneously targeting bZIP2, bZIP11 and bZIP44) were cultivated for 6h under extended night. Total RNA was extracted from whole seedlings and used for RNAseq library preparation. Overall design: Examination of global transcriptional changes in WT as well as SnRK1 and S1-bZIP knockdown lines in response to short-term dark cultivation.
Publication Title
Snf1-RELATED KINASE1-Controlled C/S<sub>1</sub>-bZIP Signaling Activates Alternative Mitochondrial Metabolic Pathways to Ensure Plant Survival in Extended Darkness.
Sample Metadata Fields
Age, Subject
View Samples- Mus musculus
- 21 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We are examining the genes that control initiation and progression of murine medulloblastomas that result from loss of patched. Approximately 25% of human medulloblastomas have mutations in patched or in other elements of the sonic hedgehog pathway. However, the cells from which these tumors originate (neural progenitors or stem cells), the cells that are responsible for tumor propagation (cancer stem cells), and the genes that are required for tumor progression are poorly understood. To address these questions, we have developed conditional patched knockout mice in which the gene is deleted in neural stem cells or progenitors. In addition, we have isolated a population of tumor-propagating cells from these tumors. By studying these models we will gain insight into the mechanisms of tumorigenesis and identify new targets for therapy.
Publication Title
Identification of CD15 as a marker for tumor-propagating cells in a mouse model of medulloblastoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
SUMMARY
Publication Title
Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
It is generally believed that cerebellar granule neurons originate exclusively from granule neuron precursors (GNPs) in the external germinal layer (EGL). Here we identify a rare population of neuronal progenitors in the developing cerebellum that expresses Nestin. Although Nestin is widely considered a marker for multipotent stem cells, these Nestin-expressing progenitors (NEPs) are committed to the granule neuron lineage. Unlike conventional GNPs, which reside in the outer EGL and proliferate extensively, NEPs reside in the deep part of the EGL and are quiescent. Expression profiling reveals that NEPs are distinct from GNPs, and in particular, express markedly reduced levels of genes associated with DNA repair. Consistent with this, upon aberrant activation of Sonic hedgehog (Shh) signaling, NEPs exhibit more severe genomic instability and give rise to tumors more efficiently than GNPs. These studies identify a novel progenitor for cerebellar granule neurons and a novel cell of origin for medulloblastoma.
Publication Title
A population of Nestin-expressing progenitors in the cerebellum exhibits increased tumorigenicity.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 39 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
We performed microarray analysis to derive gene signatures down-stream of soluble CD40 ligand stimulation in human naive B cells. Nave B cells were purified from healthy donor PBMC using negative selection beads (Miltenyi) and cultured with sCD40L at 2.5ug/ml for 6hr before microarray analysis. In the same study, cells were also harvested at day 5 post-stimulation to confirm sCD40L-induced B cell activation and proliferation. FACS analysis confirmed soluble CD40L induced up-regulation of CD86 and CD69 at 24hr. B cell proliferation was measured at day 4 post-stimulation by EdU incorporation.
Publication Title
CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 29 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
We performed microarray analysis of sCD40L-stimulated iDC to derive a signature of CD40 activation. Human monocytes from normal healthy donors were differentiated to iDCs with GM-CSF and IL4. FACS analysis demonstrated the immature status of these cells, illustrated by low expression of CD80, CD40, and CD86. We confirmed that sCD40L induces the maturation of DCs, characterized by higher expression of CD80, HLA-DR, CD86, CD83 and CD40 and secretion of pro-inflammatory cytokines at 24hr post-stimulation. Cells were harvested at 1, 3 and 24hr post-stimulation for microarray analysis.
Publication Title
CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples