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Project description:Gene expression in histologically normal epithelium from breast cancer patients and cancer-free prophylactic mastectomy patients share a similar profile Introduction: We hypothesized that gene expression in histologically normal epithelium (NlEpi) would differ in breast cancer patients (HN) compared to usual-risk controls undergoing reduction mammoplasty (RM), and that gene expression in NlEpi from cancer-free prophylactic mastectomies from high-risk women (PM), would resemble HN gene expression. Methods: We analyzed gene expression in 73 NlEpi samples microdissected from frozen tissue. In 42 cases, we used Affymetrix HU133A microarrays to compare gene expression in 18 RM vs 18 age-matched HN (9 ER+, 9 ER-) and 6 PM. Data were validated with qPCR in 31 independent NlEpi samples (8 RM, 17 HN, 6 PM). Results: 98 probesets (86 genes) were differentially expressed between RM and HN samples. Perfoming supervised hierarchical analysis with these 98 probesets, PM and HN samples clustered together, away from RM samples. qPCR validation of independent samples was high (84%) and uniform in RM vs HN, and lower (58%), but more heterogeneous, in RM vs PM. The 86 genes were implicated in many processes including transcription and the MAPK pathway. Conclusion: Gene expression differs between NlEpi of cancer cases and controls. The cancer cases' profile can be discerned in high-risk NlEpi. This suggests that the profile is not an effect of the tumor, but may mark increased risk and reveal breast cancer's earliest genomic changes. We determined that 98 probesets significantly differed between reduction mammoplasty and histologically normal epithelium from breast cancer patients. We also found that the histologically normal epithelium from prophylactic mastectomy patients' gene expression was more similar to histologically normal epithelium from breast cancer patients' than to reduction mammoplasty patients' gene expression. These results demonstrate that gene expression differs between NlEpi of cancer cases and controls. The cancer cases’ profile can be discerned in high-risk NlEpi. This suggests that the profile is not an effect of the tumor, but may mark increased risk and reveal breast cancer's earliest genomic changes.
2010-06-01 | GSE20437 | GEO
Project description:Maternal-fetal interface plays a crucial role to ensure a successful pregnancy. RM (≥3 consecutive pregnancy losses) occurring in 1-3% of fertile couples has a heterogeneous background with contribution from both genetic and environmental factors. As several physiological processes are affected in the pathogenesis of RM, it serves as a good model to study the processes at the maternal-fetal interface. We aimed to map differentially expressed genes and pathways affected in case of RM. Affymetrix® GeneChip® HG-U133 Plus 2.0 Array was applied to placental tissue from 4 RM cases (mean gestational age 63 days) and 6 elective abortions as controls (mean gestational age 62.8 days). Between the two groups 30 transcripts representing 27 genes showed differential expression. 10 genes with the highest fold-change were chosen for validation and further replicated in an independent sample set (9 RM cases, 17 controls) using Taqman® RT-qPCR. RM patients exhibited significant upregulation of two genes: apoptosis inducing ligand TRAIL (p=1.4x10-3) and S100A8 (p=7.9x10-4), encoding for inflammatory marker calprotectin. Combinatory effect of TRAIL, S100A8 and ASMTL provided a highly sensitive test distinguishing RM cases from controls (ROC analysis, area under curve=0.967). Immunohistochemical staining detected TRAIL and ASMTL mainly in trophoblastic cells and S100A8 in myeloid cells of maternal blood at maternal-fetal interface of first trimester placenta. In conclusion, genome wide expression profiling distinguished three differentially expressed genes in RM placentas: TRAIL, S100A8 and ASMTL. Although the detected gene expression alterations related to various pathways could be primary (causing) or secondary (consequence) events associated with the process of RM, the joint contribution of identified markers may provide a highly predictive test for detection of early pregnancy complications 10 gene arrays, 6 in control group and 4 in cases
2010-12-31 | E-GEOD-22490 | biostudies-arrayexpress
Project description:The National Institute of Standards and Technology (NIST) has prepared four seafood reference materials (RMs) for use in food safety and nutrition studies: wild-caught and aquacultured salmon (RM 8256 and RM 8257) and wild-caught and aquacultured shrimp (RM 8258 and RM 8259). These materials were characterized using genetic, metabolomic (1H-NMR, nuclear magnetic resonance and LC-HRMS/MS, liquid chromatography high resolution tandem mass spectrometry), lipidomic and proteomic methods to explore their use as matrix-matched, multi-omic differential materials for method development towards identifying product source and/or as quality control in untargeted omics studies. The results from experimental replicates were reproducible for each reference material and analytical method, with the most abundant features reported. Additionally, differences between the materials could be detected, where wild-caught and aquacultured seafood could be distinguished using untargeted metabolite, lipid and protein analyses. Further processing of the fresh frozen RMs by freeze-drying revealed the freeze-dried seafoods could still be reliably discerned. These results demonstrate the usefulness of these reference materials as tools for omics instrument validation and measurement harmonization in seafood-related studies. Furthermore, their use as differential quality control materials, regardless of preparation method, may also provide a tool for laboratories to demonstrate proficiency at discriminating between products based on source/species.
2023-08-21 | MSV000092716 | MassIVE
Project description:By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains. We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM. A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments. The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003). We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium. We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays. In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed. Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821). The results are part of Ronald et al. (2005) describing a novel use of oligonucleotide expression arrays to perform genotyping. This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.
2004-11-16 | GSE1975 | GEO
Project description:Gene expression in histologically normal epithelium from breast cancer patients and cancer-free prophylactic mastectomy patients share a similar profile Introduction: We hypothesized that gene expression in histologically normal epithelium (NlEpi) would differ in breast cancer patients (HN) compared to usual-risk controls undergoing reduction mammoplasty (RM), and that gene expression in NlEpi from cancer-free prophylactic mastectomies from high-risk women (PM), would resemble HN gene expression. Methods: We analyzed gene expression in 73 NlEpi samples microdissected from frozen tissue. In 42 cases, we used Affymetrix HU133A microarrays to compare gene expression in 18 RM vs 18 age-matched HN (9 ER+, 9 ER-) and 6 PM. Data were validated with qPCR in 31 independent NlEpi samples (8 RM, 17 HN, 6 PM). Results: 98 probesets (86 genes) were differentially expressed between RM and HN samples. Perfoming supervised hierarchical analysis with these 98 probesets, PM and HN samples clustered together, away from RM samples. qPCR validation of independent samples was high (84%) and uniform in RM vs HN, and lower (58%), but more heterogeneous, in RM vs PM. The 86 genes were implicated in many processes including transcription and the MAPK pathway. Conclusion: Gene expression differs between NlEpi of cancer cases and controls. The cancer cases' profile can be discerned in high-risk NlEpi. This suggests that the profile is not an effect of the tumor, but may mark increased risk and reveal breast cancer's earliest genomic changes. We determined that 98 probesets significantly differed between reduction mammoplasty and histologically normal epithelium from breast cancer patients. We also found that the histologically normal epithelium from prophylactic mastectomy patients' gene expression was more similar to histologically normal epithelium from breast cancer patients' than to reduction mammoplasty patients' gene expression. These results demonstrate that gene expression differs between NlEpi of cancer cases and controls. The cancer casesâ?? profile can be discerned in high-risk NlEpi. This suggests that the profile is not an effect of the tumor, but may mark increased risk and reveal breast cancer's earliest genomic changes. 42 total laser capture microdissected histologically normal breast tissue samples were analyzed with Affymetrix HU133A microarrays. 36 samples were age-matched between reduction mammoplasty (n=18) and histologically normal epithelial samples from breast cancer patients (n=18; 9ER+, 9ER-). 6 histologically normal epithelial samples from prophylactic mastectomy patients were then compared to data generated from the original 36 sample comparison. Sample numbers correspond to individual patient samples.
2010-06-08 | E-GEOD-20437 | biostudies-arrayexpress
Project description:By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains. We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM. A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments. The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003). We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium. We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays. In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed. Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821). The results are part of Ronald et al. (in press) describing a novel use of oligonucleotide expression arrays to perform genotyping. This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.
2008-06-11 | E-GEOD-1975 | biostudies-arrayexpress
Project description:Miscarriage occurs in 15-20% of clinical pregnancies. While chromosomal errors are observed in over 50%, causes of karyotypically normal losses are poorly understood. DNA methylation undergoes reprogramming during development and must be appropriately set to maintain a healthy pregnancy. We hypothesize that aberrant DNA methylation may cause karyotypically normal miscarriage, particularly among women experiencing recurrent miscarriage (RM). DNA methylation in first trimester chorionic villi was assessed in chromosomally normal miscarriages from women with RM (N=33) or isolated miscarriage (M, N=21), and elective terminations (TA, N=16). Differentially methylated candidate loci were identified using the Illumina Infinium HumanMethylation27 BeadChip array by comparing 10 RM to 10 TA samples. Follow up showed a significant increase in methylation in RM and M compared to TA placentae at the CYP1A2 (p=0.002) and AXL (p=0.02) promoters and decrease at the DEFB1 (p=0.008) promoter. Gene function analysis showed an enrichment of imprinted genes (p=9.53E-10) and genes previously associated with RM (p=9.51E-06). DNA methylation was evaluated at 7 imprinted loci using bisulfite pyrosequencing. An increase of outliers at these loci was observed in RM (3.9%) compared to M (0%) and TA (0.9%) (p=0.02), with increased average methylation at the H19/IGF2 ICR1 in M samples (p<0.0001). Altered DNA methylation in the placenta at specific loci, as well as global dysregulation in specific cases, may contribute to or be a consequence of placental insufficiency in karyotypically normal miscarriage.
2016-01-02 | GSE43256 | GEO
Project description:The aim of this work was to use a high density microarray approach in Streptomyces coelicolor M145 using a represive condition (RM) (0.5%agar+0.5%glucose) and non-repressive condition (NRM) (agar 1%)
2016-04-02 | E-MTAB-3603 | biostudies-arrayexpress
Project description:NIST - CosmosID Metagenomics MVP Challenge
| PRJNA495173 | ENA