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SRP054972
Mus musculus
6 Downloadable Samples
Illumina HiSeq 2000
Description
Mouse Embryonic Stem Cells (ESCs) express PDGFRa heterogeneously, fluctuating between a PDGFRa+ (PrE-primed) and a Platelet Endothelial Cell Adhesion Molecule 1 (PECAM1)-positive state (epiblast-primed). The two surface markers can be co-detected on a third subpopulation, expressing epiblast and PrE determinants. Overall design: Three different subpopulatiosn were sorted based on PECAM1/PDGFRa expression and analyzed by NGS
Publication Title
PDGFRα<sup>+</sup> Cells in Embryonic Stem Cell Cultures Represent the In Vitro Equivalent of the Pre-implantation Primitive Endoderm Precursors.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Identifying PDEF regulated genes may shed light on the mechanism by which PDEF may induce breast cancer progression. To that purpose, we have used the MCF-7 human breast tumor cell line model to identify PDEF induced genes. Briefly, PDEF expression was down regulated by shRNA in MCF-7 cells and RNA probes from PDEF-down regulated and control MCF-7 cells were used to screen the Affymetrics HG-U133A Gene Chips. This analysis found 62 genes that were induced 2-fold or higher by PDEF. Further analysis of 3 of these genes namely S100A7, CEACAM6 and B7-H4 in primary breast tumors showed CEACAM6 as a frequently elevated and co-exressed gene with PDEF in these tumors.
Publication Title
Prostate derived Ets transcription factor and Carcinoembryonic antigen related cell adhesion molecule 6 constitute a highly active oncogenic axis in breast cancer.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
To identify novel genes and adaptations induced by resveratrol preconditioning that could promote long-term cerebral ischemic tolerance. After analyzing the results, we identified only 155 differentially expressed genes among which the majority of genes consisting of 126 were downregulated and only 29 genes were upregulated. The downregulated genes clustered into biological processes involved in regulating the memebrane potential, gene expression regulation, and neurotrasmitter transport secrection. While the upregulated gene included immediate early genes and genes involved in antioxidant defense. Overall design: Mice were subject to an intraperitoneal injection of vehicle or resveratrol (10mg/kg) (n=3 per group), two weeks later their cerebral cortex was collected, RNA was extracted and then sent for sequencing
Publication Title
Resveratrol Preconditioning Induces Genomic and Metabolic Adaptations within the Long-Term Window of Cerebral Ischemic Tolerance Leading to Bioenergetic Efficiency.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 14 Downloadable Samples
- IlluminaHiSeq2000
Description
In this study we isolated and cultured neural progenitor cells (NPCs) from human fetal brain collected during the gliogenic phase (second trimester) of aborted fetuses, we differentiated NPCs into astrocyte using different protocols (FBS or CNTF/BMP4) and utilized RNA sequencing to analyze transcriptomic changes underlying the differentiation process Overall design: Neural progenitor cells (NPCs) isolated from 4 different donors (91, 103, 110 and 114 days embryos) were differentiated for 1 week using 2.5% FBS, while 3 NPCs lines (two from 103 and one from 110 days embryo) were differentiated for 1 week in the presence of CNTF/BMP4. RNA was extracted from NPCs before and after differentiation and submitted for sequencing on the Illumina HiSeq 2000 platform
Publication Title
A comparative transcriptomic analysis of astrocytes differentiation from human neural progenitor cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The data contained in this record are used to differentiate between the effects of IFN-a and IFN-b on 48h cultures of the ex vivo pbmcs of ATL patients, using Affymetrix microarrays (HuGene 1.0).
Publication Title
IFN-β induces greater antiproliferative and proapoptotic effects and increased p53 signaling compared with IFN-α in PBMCs of Adult T-cell Leukemia/Lymphoma patients.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
Glucocorticoids are first-line agents for the treatment of many eosinophil-associated disorders. However, their mechanism of action in this group of disorders remains poorly understood, including the well-known clinical observation that glucocorticoids at therapeutic doses lead to profound, transient eosinopenia within hours of administration. To gain an unbiased, genome-wide view of the early transcriptional effects of glucocorticoids on human eosinophils in vivo, and torelate them to the kinetics of glucocorticoid-induced eosinopenia, RNA sequencing was performed on purified blood eosinophils obtained before and 30, 60, and 120 minutes after administration of a single dose of oral prednisone (1 mg/kg) to healthy subjects with hypereosinophilia (hypereosinophilia of unknown significance). Overall design: Three subjects with hypereosinophilia of unknown significance were each given a single dose of oral prednisone, 1 mg/kg. Whole blood was collected before and 30 minutes, 1 hour, and 2 hours after prednisone administration. Eosinophils were purified from each peripheral blood sample. Total RNA was obtained from purified eosinophils and subject to library preparation and high-throughput sequencing.
Publication Title
Transcript- and protein-level analyses of the response of human eosinophils to glucocorticoids.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment, Subject, Time
View Samples- Homo sapiens
- 92 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Blood from subjects with cardioembolic stroke and controls was collected, and the RNA extracted was interrogated and whole genome U133 Affymetrix Arrays. Twenty-three control samples and sixty-nine cardioembolic stroke samples were assayed.
Publication Title
Gene expression in peripheral immune cells following cardioembolic stroke is sexually dimorphic.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 422 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 209 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Single nucleotide polymorphisms (SNP) can affect mRNA gene expression, in a tissue-specific manner. In this work we survey association of SNP alleles with mRNA gene expression in human dorsal root ganglions (DRG) to gain insights into pathophysiology of pain phenotypes.
Publication Title
Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 116 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Single nucleotide polymorphisms (SNP) can affect mRNA gene expression, in a tissue-specific manner. In this work we survey association of SNP alleles with mRNA gene expression in human dorsal root ganglions (DRG) to gain insights into pathophysiology of pain phenotypes.
Publication Title
Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes.
Sample Metadata Fields
Specimen part
View Samples