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GSE39976
Homo sapiens
26 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Approximately 5% of all breast cancers can be attributed to an inherited mutation in one of two cancer susceptibility genes, BRCA1 and BRCA2. We searched for genes that have the potential to distinguish healthy BRCA1 and BRCA2 mutation carriers from non-carriers based on differences in expression profiling. Using expression microarrays we compared gene expression of irradiated lymphocytes from BRCA1 and BRCA2 mutation carriers versus control non-carriers. We identified 137 probe sets in BRCA1 carriers and 1345 in BRCA2 carriers with differential gene expression. Gene Ontology analysis revealed that most of these genes relate to regulation pathways of DNA repair processes, cell cycle regulation and apoptosis. Real-time PCR was performed on the 36 genes which were most prominently differentially expressed in the microarray assay; 21 genes were shown to be significantly differentially expressed in BRCA1 or BRCA2 mutation carriers as compared to controls (p<0.05). Based on a validation study with 40 mutation carriers and 17 non-carriers, a multiplex model that included six or more coincidental genes of 18 selected genes was constructed in order to predict the risk of carrying a mutation. The results using this model showed sensitivity 95% and specificity 88%. In summary, our study provides insight into the biological effect of heterozygous mutations in BRCA1 and BRCA2 genes in response to ionizing irradiation induced DNA damage. We also suggest a set of 18 genes that can be used as a prediction and screening tool for BRCA1 or BRCA2 mutational carriers by using easily obtained lymphocytes.
Publication Title
Determination of molecular markers for BRCA1 and BRCA2 heterozygosity using gene expression profiling.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
IlluminaHiSeq2500
Description
Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and in M2 immunosuppressive macrophages. Stabilin-1 functions in scavenging, endocytosis and leukocyte adhesion to and transmigration through the endothelial cells. We have analyzed the putative functions of Stabilin-1 in blood monocytes and found that in healthy individuals 60-80% of both CD14+CD16- and CD14+C16+ monocytes, but not CD14dimCD16+ monocytes, expressed Stabilin-1 on the surface. Microarray and RNAseq analysis was performed to get more insight into the effect of Stabilin-1 expression on human monocytes transcriptome. Overall design: The transcriptome of human monocytes transfected with Stabilin-1 siRNA was compared to that of control siRNA transfected monocytes
Publication Title
Monocyte Stabilin-1 Suppresses the Activation of Th1 Lymphocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina mouse-6 v1.1 expression beadchip
Description
Vascular adhesion protein-1 (VAP-1) is an endothelial cell-surface protein. It is also an enzyme posessing semicarbazide-sensitive amine oxidase activity (EC.1.4.3.6). VAP-1 is involved in leukocyte traffic. To study the role of VAP-1 in tumor immunity, we compared gene expression profiles in melanomas growing in VAP-1 -/- mice and their wid-type littermates.
Publication Title
Vascular adhesion protein-1 enhances tumor growth by supporting recruitment of Gr-1+CD11b+ myeloid cells into tumors.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and in M2 immunosuppressive macrophages. Stabilin-1 functions in scavenging, endocytosis and leukocyte adhesion to and transmigration through the endothelial cells. Overall design: The transcriptome of liver tissue in 2wk old and E17.5 Stab1 knock-out mice was compared to that of corresponding wild type mice
Publication Title
Enhanced Antibody Production in Clever-1/Stabilin-1-Deficient Mice.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The distinction between lymphatic and blood vessels is biologically fundamental. Two immortalized cell lines, which have been widely used as models for endothelial cells of blood vascular origin, are the human microvascular endothelial cell line-1 (HMEC-1) and the telomerase-immortalized microvascular endothelial cell line (TIME). However, analysis of protein expression by flow cytometry revealed expression of lymphatic markers on these cell lines. Furthermore, functional in vitro leukocyte transmigration assays demonstrated deficiencies in several steps of the leukocyte extravasation cascade. Hence we performed this microarray analysis of the gene expression in HMEC-1 and TIME. We then compare the expression profiles to those of published blood- and lymphatic endothelial cells.
Publication Title
Plasticity of blood- and lymphatic endothelial cells and marker identification.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 42 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
The 14-week experiment included three groups: 1) the Acute Cpn group, with one C. pneumoniae inoculation at the age of 9 wks; 2) the Chronic Cpn group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; and 3) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks. The mice were sacrificed at the age of 14 wks. The 24-week experiment included four groups: 1) the recurrent A. actinomycetemcomitans infection group, with ten A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; 2) the chronic C. pneumoniae infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; 3) the combined chronic C. pneumoniae and recurrent A. actinomycetemcomitans infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks, and ten A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; and 4) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks, and ten 0.9% NaCl inoculations once a week from the age of 14 to 23 wks. The mice were sacrificed at the age of 24 wks.Epididymal and inguinal AT gene expression was analyzed using an Illumina Mouse WG-6 v2.0 platform.
Publication Title
The effect of proatherogenic pathogens on adipose tissue transcriptome and fatty acid distribution in apolipoprotein E-deficient mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Effect of fumarase point mutation or knock-out on transcriptional profile in yeast to model hereditary leiomyomatosis and renal cell cancer (HLRCC).
Publication Title
Modeling tumor predisposing FH mutations in yeast: effects on fumarase activity, growth phenotype and gene expression profile.
Sample Metadata Fields
Sex, Subject
View Samples- Mus musculus
- 17 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Lung cancers exhibit pronounced functional heterogeneity, confounding precision medicine. We studied how the cell-of-origin contributes to phenotypic heterogeneity following conditional expression of KrasG12D and loss of Lkb1 (Kras;Lkb1). Using progenitor cell type-restricted adenoviral-Cre to target cells expressing Surfactant Protein C (SPC) or club cell antigen 10 (CC10), we show that Ad5-CC10-Cre infected mice exhibit a shorter latency compared with Ad5-SPC-Cre cohorts. We further demonstrate that CC10+ cells are the predominant progenitors of adenosquamous carcinoma (ASC) tumors, and give rise to a wider spectrum of histotypes that includes mucinous and acinar adenocarcinomas. Transcriptome analysis shows ASC histotype-specific upregulation of proinflammatory and immunomodulatory genes. This is accompanied with an ASC-specific immunosuppressive environment, consisting of downregulated MHC genes, recruitment of CD11b+ Gr-1+ tumor-associated neutrophils (TANs) and decreased T-cell numbers. We conclude that progenitor cell-specific etiology influences the Kras;Lkb1-driven tumor histopathology spectrum and histotype-specific immune microenvironment.
Publication Title
Cell of Origin Links Histotype Spectrum to Immune Microenvironment Diversity in Non-small-Cell Lung Cancer Driven by Mutant Kras and Loss of Lkb1.
Sample Metadata Fields
Specimen part
View Samples- Escherichia coli
- 6 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of
Publication Title
Primary Amine Oxidase of Escherichia coli Is a Metabolic Enzyme that Can Use a Human Leukocyte Molecule as a Substrate.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Global transcriptome analysis showed that human lymphatic endothelial cells (LECs) grown on a soft matrix exhibit increased GATA2 expression, concomitant with a GATA2-dependent upregulation of genes involved in cell migration and lymphangiogenesis, including the key lymphangiogenic growth factor receptor VEGFR3.
Publication Title
Matrix stiffness controls lymphatic vessel formation through regulation of a GATA2-dependent transcriptional program.
Sample Metadata Fields
Specimen part
View Samples