Project description:Expression levels of proteins and phosphoproteins, covering major cancer signaling pathways with a special focus on breast cancer biology, were obtained for a series of 109 breast cancer tumor specimens with positive estrogen receptor status. Tumor specimens from patients diagnosed with primary invasive breast carcinoma were collected at the time of surgery between 2008 and 2010 at the Department of Gynecology and Obstetrics / National Center for Tumor Diseases Heidelberg. None of the patients had received neoadjuvant therapy. Institutional Review Board approval was received as ethics vote no. S039/2008 and informed consent was obtained from all patients. Tumor specimens were processed within 20 min after surgery. Samples were stored snap frozen at -80°C until further use. Only tumor samples with > 70% tumour cells and positive estrogen receptor status (immunoreactive score ≥ 3) as assessed by routine immunohistochemistry were selected for this study (n = 109). Tumor lysates were printed on a series of nitrocellulose coated glass slides and probed with 128 different primary antibodies directed against proteins and phosphoproteins of interest. Primary antibodies were selected to recognize proteins involved in major cancer signaling pathways with a special focus on breast cancer biology.
Project description:In addition to determining possible diagnostic and predictive peptides of lupus and CNS-lupus, we also used our microarray technology along with the Guitope computer program to determine possible natural protein match to five monoclonal autoantibodies that were created using one of the autoimmune MRL/lpr mouse. Submitter states "We have no processed data to submit. We have no gpr files to submit." Microarray analysis was performed on five monoclonal brain-reactive autoantibodies (F9, G10, G4, D1 and D9) that were created from one autoimmune mouse with altered behavior. These samples were tested in duplicated along with a control sample on the GPL17600 platform.
Project description:The screening of a previously reported fluorescein labelled 10,000 member PNA encoded peptide library allowed information on the interaction between the peptide-ligands and the cell surface receptors to be extracted, identified new peptide ligands for cell surface receptors, and gave crucial information about consensus sequences. A novel indirect amplification of the PNA signal by amplification of the PNA-complementary DNA library was developed to screen PNA-encoded peptide library against D54, HEK293T, and HEK293T-CCR6 cells. This work generates a new approach to biological discovery and an expansion of modern microarray techniques. In addition, the microarray approach facilitates screening for differences in surface-receptor ligands and/or receptor expression between various cell types including diseased and normal cells.
Project description:Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels Three immunosignatures from human Valley Fever (Coccidiodes) patients and three immunosignatures from human influenza vaccine recipients were examined to test an algorithm that extends the apparent dynamic range of a fluorescence image. These images had several saturated spots at 70PMT and 100% laser power. The program examined the differences between Valley Fever and influenza in terms of standard image processing vs. segmentation and intensity estimation.
Project description:Background: Microarray technology may offer a new opportunity to gain insight into disease-specific global protein expression profiles. The present study was performed to apply a serum cytokine-array to screen for potential molecular biomarkers for Parkinson's disease (PD), multiple system atrophy (MSA), progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS). Methodology/Principal Findings: Serum samples were obtained from patients with clinical diagnoses of PD (n=117), MSA (n=31) and PSP/CBS (n=38) and 99 controls. Cytokine profiles of sera of patients and controls were analyzed with a semiquantitative human cytokine antibody array. In a next step, significantly altered cytokines were individually validated by immunoassays. The cytokine array revealed a significantly altered expression of 12 cytokines. Immunoassay validation confirmed a significant increase of PDGF-BB in PSP/CBS, MSA and PD and a decrease of Prolactin in PD (Kruskal-Wallis p<0.05). A multivariate analysis taking into account diagnoses anti-Parkinsonian treatment, sex and age revealed that PDGF-BB levels were influenced only by the diagnoses (p<0.001), whereas Prolactin levels were influenced only by anti-Parkinsonian treatment (p<0.001). These findings could be corroborated by a subgroup analysis in untreated patients. Conclusions/Significance: In our unbiased cytokine array screening approach we found PDGF-BB to be elevated in PSP/CBS, MSA and PD. Increased PDGF-BB levels might be of relevance in a model of molecular biomarkers for Parkinsonian syndromes. Screen serum samples from patients with Parkinson's disease, progressive supranuclear palsy, corticobasal syndrome, multisystem atrophy and controls for deregulation of serum proteins using a cytokine-array detecting 174 secreted signaling proteins.
Project description:High-throughput microarray analysis of a 1296-member PNA-encoded peptide library for the identification of short homing-peptides as tools for selective delivery into specific cell types.
Project description:The aim of the study was to determine B6 and BXD2 mouse sera IgG and IgM reactivity to linear peptide epitopes at different ages. Serum from B6 or BXD2 mice was diluted at 1:200 for IgG-specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens. 80 pre-selected peptides based on a previous screen of pooled mouse serum BXD2 against the PEPperCHIP® Autoimmunity Microarray with 2,733 linear B-cell epitopes were printed in duplicate in 16 copies on a custom PEPperCHIP® Peptide Microarray. Flag (DYKDDDDKGG) and HA (YPYDVPDYAG) control peptides (10 spots each control) were randomly distributed in each array copy as controls. Sera from 2, 5, or 9 month old B6 or BXD2 mice was profiled for anti-mouse IgG or IgM-specific analysis of autoantibody reactivity to the peptide auto-epitopes.
Project description:The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens Pooled sera from three 6-9 month old B6 mice was profiled for IgG or IgM-specific analysis of autoantibody reactivity to peptide auto-epitopes printed in duplicate on a PepperPrint Chip.
Project description:The aim of the array was to determine the BXD2 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old BXD2 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens In this study, pooled sera from three 6-9 month old BXD2 mice was profiled for IgG and IgM specific autoantibody reactivity to peptide auto-epitopes printed in duplicate on a PepperPrint Chip.
Project description:An experiment was designed to use a computer program to create lithography masks using a pseudo-random pattern generator. The data in this file are results from immunosignaturing 8 different monoclonals using a 10,000 peptide random-sequence microarray. Peptides were synthesized by Sigma Aldrich, and printed onto glass slides and used to test several different parameters. One replicate of each peptide was printed on 1 CIM_10K_v2 peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.