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GSE74140
Mus musculus
6 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Low levels of MYB promote the development of myeloproliferative neoplasm (MPN). The cell type identified that can transplant the MPN phenotype has been identified as expressing KIT, CD11b and low levels of lineage markers (K11bL).
Publication Title
Transcriptional regulation of SPROUTY2 by MYB influences myeloid cell proliferation and stem cell properties by enhancing responsiveness to IL-3.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 110 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
It is widely accepted that a womans lifetime risk of developing breast cancer at menopause is reduced by early full term pregnancy and multiparity. This phenomenon is associated with the development and differentiation of the breast, which ultimately imprints a specific genomic profile in the mammary epithelium. In the present work we demonstrate that this profile represents a permanent signature that could be associated with the breast cancer risk reduction conferred by pregnancy.
Publication Title
Defining the genomic signature of the parous breast.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
IlluminaHiSeq2000
Description
This experiment aims to identify the biological pathways and diseases associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells (PBMCs). Overall design: The experiment comprised of samples obtained from 3 healthy donors. The expression profiles of in vitro IL-13 stimulation were generated using RNA-seq technology for 3 PBMC samples at 24 hours. The transcriptional profiles of PBMCs without IL-13 stimulation were also generated to be used as controls. An IL-13R-alpha antagonist (Redpath et al. Biochemical Journal, 2013) was introduced into IL-13 stimulated PBMCs and the gene expression levels after 24h were profiled to examine the neutralization of IL-13 signaling by the antagonist.
Publication Title
Combining multiple tools outperforms individual methods in gene set enrichment analyses.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Despite the fact that clinically relevant infectious agents such as human immunodeficiency virus enter through the intestinal mucosa, the intestinal T cell response to infection remains understudied. Listeria monocytogenes (LM) has been used as a model organism for studying T cell responses and the normal route of infection for LM and a potential route for use of LM as a vaccine are through ingestion. Nevertheless, the vast majority of LM immunological studies utilize inoculation routes other than oral. Moreover in the bacterial strains used the internalin. A protein binds human E-cadherin with high affinity but poorly binds mouse E-cadherin. This receptor-ligand pairing is required for entry of LM into intestinal epithelial cells. The oral infection studies proposed here utilize a recombinant LM that expresses an internalin A protein with high affinity for mouse E-cadherin. Thus, the physiologic route and entry point of LM is recapitulated in our studies. Our preliminary studies revealed a remarkable mucosal TCR gd T cell response to oral LM infection, whose kinetics mimic an adaptive T cell response. Most importantly, this phenotypically and functionally distinct subset of mucosal TCR gd T cells are retained long-term and undergo a recall response upon challenge. The hypothesis to be tested in this proposal is that this specialized subset of putative memory TCR gd T cells is important for protection against LM infection and also regulates the long-term protective CD8 TCR ab response. This hypothesis will be tested in the following specific aims: Aim 1. To test whether a subset of TCR gd represent bona fide mucosal memory cells. A detailed kinetic, phenotypic and functional analysis of the primary and secondary TCR gd cell response to oral LM infection will be undertaken. Aim 2. To determine the requirements for mucosal TCRgd activation in response to LM infection. Here we will test the role of dendritic cells, cosfimulation and cytokines in mounting primary and secondary TCR gd cell responses. Aim 3. To visualize the mucosal TCR gd cell response to oral LM infection. The oral infection system provides an exceptional opportunity to examine the anatomy of the mucosal TCR gd cell response.
Publication Title
γδ T cells exhibit multifunctional and protective memory in intestinal tissues.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Human pluripotent stem cells (hPSC) exposed to BMP4 (B) and inhibitors of ACTIVIN signaling (A83-01; A) and FGF2 (PD173074; P) in absence of FGF2 (BAP conditions) differentiate into colonies primarily comprised of trophoblast. In an attempt to isolate trophoblast stem cells, colonies of hESC were exposed to BAP for 24 h at which time they had begun to transition into a CDX2-positive state. Cultures were then dissociated into single cells by trypsin and grown on a gelatin substratum. Under these conditions, organized CDX2+/KRT7- colonies began to emerge within a few days. The self-renewing cell lines were not TBSC, but met standard criteria for pluripotency. They were named H1BP cells. They differed from the progenitor hPSC in morphology, ability to be clonally propagated from single cells onto gelatin, requirements for FGF2, and transcriptome profile.
Publication Title
Heightened potency of human pluripotent stem cell lines created by transient BMP4 exposure.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In human breast cancers, a phenotypically distinct minority population of tumorigenic cancer (TG) cells (sometimes referred to as cancer stem cells) drives tumor growth when transplanted into immunodeficient mice. Our objective was to identify a mouse model of breast cancer stem cells that could have relevance to studying human breast cancer. To do so, we utilized breast tumors of the MMTVWnt-1 mice. MMTV-Wnt-1 breast tumors were harvested, dissociated into single cell suspensions, and FACS sorted on Thy1, CD24, and CD45. FACS sorted cells were then injected into recipient background FBV/NJ female mice. Thy1+CD24+ cancer cells, which constitute approximately 1-4% of tumor cells were highly enriched for cells capable of regenerating new tumors when compared to cells of the tumor that did not fit this profile (Not Thy1+CD24+). Resultant tumors were of the same phenotypic diversity as the original tumor and behaved in a similar manner when passaged. Microarray analysis comparing Thy1+CD24+ tumor cells to Not Thy1+CD24+ cells identified a list of differentially expressed genes. Orthologs of these differentially expressed genes predicted survival of human breast cancer patients from two different study groups. These studies suggest that there is a cancer stem cell compartment in the MMTV-Wnt-1 murine breast tumor and that there is a clinical utility of this model for the study of cancer stem cells.
Publication Title
Isolation and molecular characterization of cancer stem cells in MMTV-Wnt-1 murine breast tumors.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Breast cancers contain a minority population of cancer cells characterized by CD44 expression but low or undetectable levels of CD24 (CD44+CD24-/low) that have higher tumorigenic capacity than other subtypes of cancer cells. METHODS: We compared the gene-expression profile of CD44+CD24-/low tumorigenic breast-cancer cells with that of normal breast epithelium. Differentially expressed genes were used to generate a 186-gene invasiveness gene signature (IGS), which was evaluated for its association with overall survival and metastasis-free survival in patients with breast cancer or other types of cancer. RESULTS: There was a significant association between the IGS and both overall and metastasis-free survival (P<0.001, for both) in patients with breast cancer, which was independent of established clinical and pathological variables. When combined with the prognostic criteria of the National Institutes of Health, the IGS was used to stratify patients with high-risk early breast cancer into prognostic categories (good or poor); among patients with a good prognosis, the 10-year rate of metastasis-free survival was 81%, and among those with a poor prognosis, it was 57%. The IGS was also associated with the prognosis in medulloblastoma (P=0.004), lung cancer (P=0.03), and prostate cancer (P=0.01). The prognostic power of the IGS was increased when combined with the wound-response (WR) signature. CONCLUSIONS: The IGS is strongly associated with metastasis-free survival and overall survival for four different types of tumors. This genetic signature of tumorigenic breast-cancer cells was even more strongly associated with clinical outcomes when combined with the WR signature in breast cancer.
Publication Title
The prognostic role of a gene signature from tumorigenic breast-cancer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Newborn Balb/c mice were injected with 1.5x10^6 fluorescent-forming units (ffu) of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth to induce experimental model of biliary atresia. The extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after rhesus rotavirus or saline injection. GeneChip Mouse Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was differently regulated after rhusus rotavirus injection compare to the normal saline controls.
Publication Title
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice
Publication Title
Correction of MFG-E8 Resolves Inflammation and Promotes Cutaneous Wound Healing in Diabetes.
Sample Metadata Fields
Specimen part
View Samples