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GSE21655
Homo sapiens
21 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Induced pluripotent stem cells (iPSCs) have been generated from various somatic cells under feeder-layer conditions. These feeder-derived iPSCs generated in different labs exhibit greater variability than between different traditional embryo derived hESC lines. For that reason, it is important to develop a standard and defined system for deriving autologous patient stem cells. We have generated iPSCs under feeder-free conditions using Matrigel coated vessels in chemically defined medium, mTeSR1. These feeder-free derived iPSCs are in many ways similar to feeder-derived iPSCs and also to hESCs, with respect to their pluripotent gene expression (OCT4, NANOG, SOX2), protein expression (OCT4, NANOG, SSEA4, TRA160) and differentiation capabilities.
Publication Title
Human induced pluripotent stem cells derived under feeder-free conditions display unique cell cycle and DNA replication gene profiles.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 32 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Purpose: The management of adrenocortical tumors (ACTs) is complex, compounded by the difficulty in discriminating benign from malignant tumors using conventional histology. The Weiss score is the current most widely used system for ACT diagnosis but it has limitations, particularly with ACTs with a score of 3. The am of this study was to identify molecular markers whose expression can discriminate adrenocortical carcinomas (ACCs) from adrenocortical adenomas (ACAs) by microarray gene expression profiling and to determine their clinical applicability by using immunohistochemistry (IHC). Experimental design: Microarray gene expression profiling was used to identify 7 molecular markers which were significantly differentially expressed between ACCs and ACAs. These results were confirmed with quantitative PCR for all 7 genes and IHC for 3 protein. Results: Microarray gene expression profiling was able to accurately categorize ACTs into ACCs and ACAs. All 7 genes were strong discriminators of ACCs from ACAs on qPCR. IHC with IGF2, MAD2L1, CCNB1 and Ki-67, but not ACADVL or ALOX15B, had high diagnostic accuracy in differentiating ACCs from ACAs. The best results however were obtained with a combination of IGF2 and Ki-67 with 96% sensitivity and 100% specificity in diagnosing ACCs. Conclusion: Microarray gene expression profiling accurately differentiates ACCs from ACAs. The combination of IGF2 and Ki-67 IHC is also highly accurate in distinguishing between the 2 groups and is particularly helpful in ACTs with Weiss score of 3.
Publication Title
Microarray gene expression and immunohistochemistry analyses of adrenocortical tumors identify IGF2 and Ki-67 as useful in differentiating carcinomas from adenomas.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Anthrax lethal toxin directly targets human peripheral monocytes and causes multiple aberrant gene responses that would be expected to result in defects in human monocytes normal signaling transduction pathways and nction. This study provides further insights into the mechanisms associated with the host immune system collapse during an anthrax infection, and suggests that anthrax LT may have additional targets outside the well-known MAPK pathway.
Publication Title
Bacillus anthracis' lethal toxin induces broad transcriptional responses in human peripheral monocytes.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Macrophage aging is pathogenic in numerous diseases, including age-related macular degeneration. Although prior studies have explored the functional consequences of macrophage aging, less is known about its cellular basis or what defines the transition from physiologic aging to disease. The purpose of this experiment was to characterize the transcriptomic changes associated with macrophage aging.
Publication Title
Oxysterol Signatures Distinguish Age-Related Macular Degeneration from Physiologic Aging.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 32 Downloadable Samples
NextSeq 500
Description
Because of the extensive data in mice supporting the concept that ST2+ Tregs might have desirable therapeutic properties, including tissue repair function, high suppressive capacity, and enhanced stability, we engineered human blood Tregs to constitutively express ST2 (IL-33R). Here we used RNA sequencing to explore the effects of short-term culture with IL-33 on human ST2-transduced Tregs. Overall design: Human naive Tregs flow-sorted from 4 independent donors were lentivirally transduced with ST2, expanded for 13 days, then stimulated with IL-2 and TCR (16 h) or IL-2, TCR, and IL-33 (16 h).
Publication Title
Innate Control of Tissue-Reparative Human Regulatory T Cells.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 117 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We collected airway epithelial brushings for microarray analysis from 42 asthmatics and two control groups 28 healthy subjects and 16 smokers. A subgroup of 32 asthmatics completed a randomized placebo-controlled trial of fluticasone propionate in which collection of brushings was repeated after 1 week of treatment.
Publication Title
Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids.
Sample Metadata Fields
Disease
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: To gain further mechanistic insight into phenotypic differences between wild type pancreatic islets and islets with loss of function of 4 Box C/D snoRNAs from the Rpl13a locus (U32a, U33, U34 and U35a). Methods:High quality total RNA (RIN = 8.5) was prepared from hand-picked islets (n = 4 mice/genotype) using TRIZOL reagent, treated with Turbo DNAse (Thermo Fisher), and used to prepare SeqPlex RNAseq libraries (Sigma). Sequencing was performed by the Washington University Genome Technology Access Center using two lanes of Illumina HiSeq 2500, 1x50. Reads were demultiplexed and trimmed, and STAR alignment and quantification analysis was carried out using the Partek Flow platform. Uniquely aligned reads were quantified to identify genes with at least a two-fold change between genotypes with p < 0.05 and FDR step-up of 0.05. Results:We observed 2-fold or greater differences in the expression of only six genes. Conclusions: Our data indicate that loss-of-function of snoRNAs from the Rpl13a locus is associated with modest changes in mRNA abundance. Overall design: Examination of murine pancreatic islet mRNA differential expression between wild type mice and mice with loss-of-function of U32a, U33, U34, and U35a snoRNAs.
Publication Title
Rpl13a small nucleolar RNAs regulate systemic glucose metabolism.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 35 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Acute rejection in cardiac transplant patients is still a contributing factor to limited survival of the implanted heart. Currently there are no biomarkers in clinical use that can predict, at the time of transplantation, the likelihood of post-transplantation acute rejection, which would be of great importance for personalizing immunosuppressive treatment. Within the Biomarkers in Transplantation initiative, the predictive biomarker discovery focused on data and samples collected before or during transplantation such as: clinical variables, genes and proteins from the recipient, and genes from the donor. Based on this study, the best predictive biomarker panel contains genes from the recipient whole blood and from donor endomyocardial tissue and has an estimated area under the curve of 0.90. This biomarker panel provides clinically relevant prediction power and may help personalize immunosuppressive treatment and frequency of rejection monitoring.
Publication Title
Predicting acute cardiac rejection from donor heart and pre-transplant recipient blood gene expression.
Sample Metadata Fields
Sex, Age, Specimen part, Race
View Samples- Mus musculus
- 24 Downloadable Samples
- Sentrix MouseRef-8 Expression BeadChip (Target ID)
Description
We examined early and late gene expression changes using the IT LPS model of Acute Lung Injury (ALI). In this model, injury peaks at day 4 and is almost completely resolved by day 10 in wild type (WT) C57BL/6 mice. In contrast to the pattern in WT mice, lymphocyte-deficient Rag-1 -/- mice exhibit strikingly delayed resolution despite similar initial injury.
Publication Title
Regulatory T cell-mediated resolution of lung injury: identification of potential target genes via expression profiling.
Sample Metadata Fields
Sex, Specimen part, Treatment, Time
View Samples- Homo sapiens
- 4 Downloadable Samples
Description
The polycomb repressive complex 2 (PRC2) histone methyl-transferase plays a central role in epigenetic regulation in development and in cancer, and hence to interrogate its role in a specific developmental transition, methods are needed for disrupting function of the complex with high temporal and spatial precision. The catalytic and substrate recognition functions of PRC2 are coupled by binding of the N-terminal helix of the Ezh2 methylase to an extended groove on the EED trimethyl lysine binding subunit. Disrupting PRC2 function can in principle be achieved by blocking this single interaction, but there are few approaches for blocking specific protein-protein interactions in living cells and organisms. Here, we describe the computational design of proteins that bind to the EZH2 interaction site on EED with sub-nanomolar affinity in vitro and form tight and specific complexes with EED in living cells. Induction of the EED binding proteins abolishes H3K27 methylation in human embryonic stem cells (hESC) and at all but the earliest stage blocks self-renewal, pinpointing the first critical repressive H3K27me3 marks in development. Overall design: 1 biological sample were isolated from naïve hESC cell line Elf1 and Elf1 expressing EED binder 22.2. RNA-seq and ChIP-seq (H3K27me3) was performed for each sample.
Publication Title
First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.
Sample Metadata Fields
No sample metadata fields
View Samples