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GSE16547
Homo sapiens
7 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognizable by its distinctive red skin lesions. The lesions are KSHV infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. Here we examine KSHVs modulation of Notch signaling using wild-type LEC cells co-cultured with DLL4 and JAG1 expressing LEC cells.
Publication Title
KSHV manipulates Notch signaling by DLL4 and JAG1 to alter cell cycle genes in lymphatic endothelia.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 20 Downloadable Samples
Illumina HiSeq 3000
Description
Transcriptomic profiling of miR-132/212-deficient and WT CD4 T cells isolated from spleens of L donovani infected mice (d28) to determine the effects of miR-132/212 on CD4 T cell activation in vivo. This was combined by transcriptomic analysis of early stage in vitro activated WT and miR-132/212-deficient CD4 T cells to identify direct miR-132/212 targets in CD4 T cells. Overall design: Examination of expression profiles of splenic CD4+ T cells from L. donovani-infected WT (samples 1-4) and miR-132/212-/- mice (samples 5-9) using RNASeq. This was followed by similar RNASeq in naïve CD4+ T-cells in WT and miR-132/212 -/- mice prior to and following 18h of in vitro TCR stimulation under Th1 conditions (samples 10-25).
Publication Title
<i>Malat1</i> Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 36 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The effects of KSHV infection of both LEC and BEC were assayed using Affymetrix hgu133plus2 chips at 72 hours post infection.
Publication Title
KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The KSHV virus expresses multiple microRNA in a single cluster. Here we test the effects of this KSHV microRNA cluster in LEC cells using Affymetrix hgu133plus2 chips.
Publication Title
KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The KSHV virus expresses multiple MAF-downregulating microRNA. Here we test the effects of MAF silencing by siRNA in LEC cells using Affymetrix hgu133plus2 chips.
Publication Title
KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 48 Downloadable Samples
- Illumina HiSeq 2500
Description
Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor interactions. Targeting ligand-receptor interactions, for instance with immune check-point inhibitors, can provide significant benefit for patients. However, our knowledge of which interactions occur in a tumor and how these interactions affect outcome is still limited. We present an approach to characterize communication by ligand-receptor interactions across all cell types in a microenvironment using single-cell RNA sequencing. We apply this approach to identify and compare ligand-receptor interactions present in six syngeneic mouse tumor models. To identify interactions potentially associated with outcome, we regress interactions against phenotypic measurements of tumor growth rate. In addition, we quantify ligand-receptor interactions between T-cell subsets and their relation to immune infiltration using a publicly available human melanoma data-set. Overall, this approach provides a tool for studying cell-cell interactions, their variability across tumors, and their relationship to outcome. Overall design: We used three different types of immuno-competent inbred mouse strains: BALB/c, and A/J z. All animals enrolled in our study were 6-8 weeks old female mice that were housed in vivarium under specific pathogen free conditions in cages of up to 5 animals and receiving special rodent diet (Teklad). We implanted two mice for each syngeneic model resulting in a total of 12 samples. Each mouse tumor was harvested when the tumor size reached 100 – 200 mm3. Each sample was minced and digested with reagents from Mouse Tumor Dissociation Kit (Miltenyi) according to the manufacturer's instructions. Cells were resuspended at 2x105 cells/mL in PBS-0.04% BSA. Each sample was processed individually and run in technical duplicates. For each sample (except CT26 and MC-38) one replicate was enriched for CD45 positive cells. Live CD45 positive cells were sorted with BD Aria after staining with FITC-CD45 (Biolegend) and 7-AAD. Single cell suspensions of all samples were resuspended in PBS-0.04% BSA at 5x105 cells/mL and barcoded with a 10x Chromium Controller (10x Genomics). In total, this procedure resulted in 24 samples.
Publication Title
Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 57 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We have made use of the E-myc transgenic mouse, a model for the study of B-cell lymphoma development that is initiated through a defined genetic alteration, to explore the contributions of additional somatic alterations that contribute to the heterogeneity of the resulting tumors. As one example of such heterogeneity, we have focused on the observation that lymphomas develop in E-myc mice with a variable time of onset. Twenty-five early-onset, 25 late-onset lymphomas and 10 normal samples were each assayed on an Affymetrix Mouse Genome 430 2.0 array.
Publication Title
Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
To identify regulation of genes involved in lipid and glycogen metabolism by PGC-1alpha
Publication Title
Suppression of PGC-1α Is Critical for Reprogramming Oxidative Metabolism in Renal Cell Carcinoma.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Danio rerio
- 54 Downloadable Samples
- IlluminaHiSeq2000
Description
Development is a complex and well-defined process characterized by rapid cell proliferation and apoptosis. At this stage in life, a developmentally young organism is more sensitive to toxicants and other stressors when compared to an adult. In response to pro-oxidant exposure, members of the Cap’n’Collar (CNC) basic leucine zipper (b-ZIP) transcription factor family (including the Nfe2-related factors, Nrfs) activate the expression of genes that contribute to reduced toxicity. Here, we studied the role of the Nrf protein, Nfe2, in the developmental response to pro-oxidant exposure in the zebrafish. Following acute waterborne exposures to diquat or tert-buytlhydroperoxide (tBOOH) at three developmental stages, wildtype (WT) and nfe2 knockout (KO) embryos and larvae were morphologically scored and their transcriptomes sequenced. Overall design: Wildtype animals were on the AB background and an additional germline nfe2 knockout strain were created by disruption of the nfe2 reading frame. Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hours post fertilization (hpf), 48hpf, and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment, 20µM diquat or 1mM tBOOH for a 4-hour dosing period. Total RNA was isolated from pooled animals and 50 bp, paired end, libraries were sequenced using the Illumina HiSeq 2000 platform, with approximately 25 million reads per sample. Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 and raw counts data normalized using DESeq2. Gene annotation was from Ensemble for GRCz10.
Publication Title
The transcription factor, Nuclear factor, erythroid 2 (Nfe2), is a regulator of the oxidative stress response during Danio rerio development.
Sample Metadata Fields
No sample metadata fields
View Samples