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SRP162522
Mus musculus
6 Downloadable Samples
Illumina HiSeq 2500
Description
Malignancies arising from mutation of tumor suppressor genes display an unexplained tissue proclivity. For example, tumor suppressor BAP1 encodes a ubiquitously expressed deubiquitinase for histone H2A but germline mutations predominantly cause uveal melanomas and mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells, fibroblasts, liver and pancreas, whereas melanocytes and mesothelial cells remain viable. E3 ligase RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient cells by suppressing the pro-survival genes Bcl-2 and Mcl-1. Our data argue that BAP1 modulates gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in cells that do not engage an RNF2-dependent apoptotic program. We propose that intolerance of BAP1 loss, and perhaps the loss of other tumor suppressors, restricts the mutant tumor spectrum. Overall design: RNA was extracted from following genotypes - BAP1 wt (WT) and BAP1 knockout (BAP1 KO).
Publication Title
Intrinsic apoptosis shapes the tumor spectrum linked to inactivation of the deubiquitinase BAP1.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
Ubiquilins are a family of proteins involved in proteasomal degradation of mislocalized membrane proteins. Here, Greer et al. demonstrate that Ubqln1 is required for BCR-driven B cell proliferation through maintenance of protein synthesis following stimulation. In the absence of Ubqln1, mitochondrial proteins accumulate in the cytosol, which may account for the observed proteostasis. BCR stimulation of murine B cells induced a long-lasting mitochondrial depolarization that did not occur in response to LPS. We hypothesize that in the absence of Ubqln1, mitochondrial depolarization leads to an accumulation of mitochondrial membrane proteins in the cytosol, which leads to translational inhibition and a cell cycle block. Overall design: For RNASeq, cells were stimulated in triplicate in 2*10e6 cells/mL for 4 hours with either 10 µg/mL anti-IgM F(ab)2 or 20 µg/mL LPS, or no stimulation. There were 18 total samples, 9 Knockout samples, 9 WT samples, 3 biological replicates per treatment group: no stimulation, 10 ug/mL a-Igm, 20 ug/mL LPS.
Publication Title
Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 21 Downloadable Samples
- Illumina HiSeq 2500
Description
The prevailing dogma that approximately 50% of our genome is “junk” DNA composed of transposable elements and retroviral insertions has recently been challenged. It has become evident that our genome has taken advantage of these transposable elements and uses them as a source of DNA to generate novel genes, which subsequently allow the organism to evolve. This process is termed “domestication of transposable elements” and the majority of these genes have been found to be essential for the existence of the organism. One of these developmentally essential domesticated genes: Peg10 (paternally expressed gene 10), was derived from a Ty3/gyspy LTR retrotransposon, yet lost its ability to transpose due to mutational events during its domestication. Remarkably, Peg10 has successfully maintained its Gag and Pol-like domains for millions of years. Peg10 orthologues are expressed in eutherian mammals and are essential for placentogenesis. To address the functional mechanisms of Peg10 we studied it in Trophoblast Stem Cells (TSCs). We find that the Gag of Peg10 is fully active: it promotes budding of vesicles, akin to the viral counterpart that catalyzes the budding of viruses. TSCs, deleted for Peg10, fail to differentiate into placental lineages, underscoring a critical role in lineage specification. This paper discusses our efforts to characterize the contents of Peg10 vesicles and whether such vesicles regulate lineage specification. Overall design: RNA was extracted from following genotypes - wildtype TSCs (WT_TSC), Peg10 knockout TSCs (KO_TSC), wildtype TSCs differentiated in 20% oxygen (WT_TSC_diff), Peg10 knockout TSCs differentiated in 20% oxygen (KO_TSC_diff), wildtype TSCs differentiated in 2% oxygen (WT_diff_2O2),and Peg10 knockout TSCs differentiated in 2% oxygen (KO_diff_2O2). Cells are kept in the pluripotent state by growing them on CellStart/Fgf4/Heparin. The cells were differentiated in two different conditions: 20% oxygen and 2% oxygen. The samples were collected at 10th day following differentiation. Cells are harvested and RNA is isolated using the Qiagen RNeasy kit. RT-PCR was performed for several differentiation markers to validate the success of the assay.
Publication Title
The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification.
Sample Metadata Fields
Specimen part, Subject
View Samples- Escherichia coli
- 15 Downloadable Samples
Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Comparison of gene expression profile of E. coli 83972 grown in minimal lab media, in urine and in 3 individual patients.
Publication Title
Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract.
Sample Metadata Fields
No sample metadata fields
View Samples- Hordeum vulgare
- 21 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Detection of single feature polymorphisms comparing five barley genotypes. Gene expression under unstressed and drought stressed conditions.
Publication Title
Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
We used microarray to compare global gene expression profiles between 5 GNAQ/11 mutant uveal melanoma cell lines (GNAQ mutant: 92-1, omm1.3, mel270; GNA11 mutant: omm-gn11 and upmd-1) and 5 GNAQ/11 wild type melanoma cell lines(sk-mel-2, mm415, mm485, sk-mel-5 and mum2c). Uveal melanoma is the most common intraocular tumor that mainly metastasizes to the liver in about 50% patients. Over 80% of UMs harbor GNAQ or GNA11 activating mutation. Currently there is no effective treatment available for UM patients. Results provide insights into downstream signaling of oncogenic GNAQ/11 and identification of therapeutic targets in UM.
Publication Title
RasGRP3 Mediates MAPK Pathway Activation in GNAQ Mutant Uveal Melanoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Identification of genes differentially expressed in roots of Arabidopsis Col-0 and ndr1-1 mutants 48 h post inoculation with the fungal pathogen Verticillium longisporum.
Publication Title
Susceptibility to Verticillium longisporum is linked to monoterpene production by TPS23/27 in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Homo sapiens
- 17 Downloadable Samples
- Illumina humanRef-8 v2.0 expression beadchip
Description
The in vitro effect of infection with different strains of Toxoplasma gondii was tested 24 hours after infection of Human Foreskin Fibroblasts (HFF)
Publication Title
Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus, Homo sapiens
- 25 Downloadable Samples
Illumina HumanRef-8 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Differential induction of TLR3-dependent innate immune signaling by closely related parasite species.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 13 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
The closely related protozoan parasites Toxoplasma gondii and Neospora caninum display similar life cycles, subcellular ultrastructure, invasion mechanisms, metabolic pathways, and genome organization, but differ in their host range and disease pathogenesis. Type II () interferon has long been known to be the major mediator of innate and adaptive immunity to Toxoplasma infection, but genome-wide expression profiling of infected host cells indicates that Neospora is a potent activator of the type I (/) interferon pathways typically associated with antiviral responses. Infection of macrophages from mice with targeted deletions in various innate sensing genes demonstrates that host responses to Neospora are dependent on the toll-like receptor Tlr3 and the adapter protein Trif. Consistent with this observation, RNA from Neospora elicits TLR3-dependent type I interferon responses when targeted to the host endo-lysosomal system. Although live Toxoplasma fail to induce type I interferon, heat-killed parasites do trigger this response, albeit much weaker than Neospora, and co-infection studies reveal that T. gondii actively suppresses the production of type I interferon. These findings reveal that eukaryotic pathogens can be potent inducers of type I interferon and that related parasite species interact with this pathway in distinct ways.
Publication Title
Differential induction of TLR3-dependent innate immune signaling by closely related parasite species.
Sample Metadata Fields
Specimen part, Cell line
View Samples