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SRP108050
Danio rerio
6 Downloadable Samples
Illumina HiSeq 2500
Description
Puberty is a special transition period in sexual maturation, and it has been extensively studied in vertebrates in the past decades. In mammals, the initiation of puberty involves activation of numerous genes; however, there have been few comprehensive reports in small model teleosts such as the zebrafish. In the zebrafish, the onset of puberty in females is marked by the appearance of the first wave of pre-vitellogenic (PV) follicles in the ovary during sexual maturation. Using transcriptomics and real-time qPCR, this study was undertaken to investigate temporal gene expression differences between the primary growth (PG) follicles and pre-vitellogenic (PV) follicles, with particular emphasis on oocyte and follicular cell specific genes as well as several closely associated signaling pathways. Our results showed that totally 1082 genes were significantly upregulated and 530 evidently downregulated during the PG-PV transition, and among them were some well recognized biomarkers such as cyp19a1a, fshr, inha and inhbaa and some novel genes like notch3, amh, gadd45ga and lpl. Further gene ontology analysis showed that egg coat formation and steroid hormone mediated signaling pathway might be critical for follicle activation from PG to PV stage. In addition, KEGG identified several signaling pathways that might play pivotal roles in early folliculogenesis, including phosphatidylinositol signaling system, glycolsaminoglycan biosynthesis, RNA transport, and p53 signaling pathways. Overall, this study reported a comprehensive analysis for biomarker genes and potential pathways involved in PG-PV transition or follicle activation, which also marks female puberty onset in the zebrafish when occurring for the first time in sexual maturation. Overall design: Examination of gene expression patterns in 2 different stage follicles (PG and PV follicles)
Publication Title
Transcriptomic Analysis for Differentially Expressed Genes in Ovarian Follicle Activation in the Zebrafish.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 15 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Human dendritic cells (DC) are suppressed by tumor-derived alpha fetoprotein (AFP), but less so by cord blood-derived normal AFP.
Publication Title
Tumor-derived α-fetoprotein impairs the differentiation and T cell stimulatory activity of human dendritic cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
To determine if there are differences in the gene expression profile of peripheral blood mononuclear cells in patients with Acute Myeloid Leukemia (AML) or Myelodysplastic Syndrome (MDS) who responded to CPI-613 when compared to those patients who did not respond we generated gene expression profiles from four responding patients and compared them to four non-responders. None of the gene expression profiles have been previously published. Here we describe the origins and provide associated clinical annotations with the hope that other investigators will be able to utilize this data in their own research.
Publication Title
A phase I study of the first-in-class antimitochondrial metabolism agent, CPI-613, in patients with advanced hematologic malignancies.
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We assessed vastus lateralis muscle gene expression levels of 12 women with the metabolic syndrome before and after a 6 month exercise training program
Publication Title
Upregulation of skeletal muscle inflammatory genes links inflammation with insulin resistance in women with the metabolic syndrome.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment, Subject, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Identification of intrathymic Eomes+ natural Th1 cells creates a novel idea that there is more than one way for the generation of innate CD4 T cells. To more deeply characterize this type of innate T cells, we compared the gene expression profile between nTh1 cells generated in CIITAtg mice and classic Th1 cells differentiated from naive CD4 T cells in Th1-polarizing condition.
Publication Title
Thymic low affinity/avidity interaction selects natural Th1 cells.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The leg of healthy volunteers was locally deconditioned using three weeks of unilateral lower limb suspension (ULLS). The extremely deconditioned legs of subjects with a spinal cord injury (SCI) were trained using eight weeks of functional electrical stimulation (FES) exercise, 2-3 times per week (total 20 sessions).
Publication Title
Expression of genes involved in fatty acid transport and insulin signaling is altered by physical inactivity and exercise training in human skeletal muscle.
Sample Metadata Fields
Subject, Time
View Samples- Rattus norvegicus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
In rats, learning and memory performance decline during normal aging, which makes this rodent species a suitable model to evaluate therapeutic strategies. In aging rats, insulin-like growth factor-I (IGF-I), is known to significantly improve spatial memory accuracy as compared to control counterparts. A constellation of gene expression changes underlie the hippocampal phenotype of aging but no studies on the effects of IGF-I on the hippocampal transcriptome of old rodents have been documented. Here, we assessed the effects of IGF-I gene therapy on spatial memory performance in old female rats and compared them with changes in the hippocampal transcriptome. Overall design: Hippocampal RNA-Seq profiles of 28 months old rats intracerebroventricularly injected with an adenovector expressing rat IGF-I was compared with placebo adenovector-injected counterparts (4 samples each group)
Publication Title
IGF-I Gene Therapy in Aging Rats Modulates Hippocampal Genes Relevant to Memory Function.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Regulatory T cells (Tregs) are critical for maintaining self-tolerance and immune homeostasis, but their suppressive function can impede effective anti-tumor immune responses. Foxp3 is a transcription factor expressed in Tregs that is required for their function. The pathways and microenvironmental cues governing Foxp3 expression and Treg function are not completely understood. We found that Yes-associated protein (YAP), a co-activator of the Hippo pathway, is highly expressed in Tregs and bolsters Foxp3 expression and Treg function in vitro and in vivo. To assess how YAP influences patterns of gene expression in Tregs, naïve CD4+ T cells and Tregs were isolated from wild type mice and CD4+ T cell lineage-restricted YAP knockout mice (YAPflox/flox, CD4-Cre+). Gene expression by naïve CD4+ T cells and their resting and stimulated Treg counterparts was analyzed by RNASeq. Our findings reveal that YAP ablation undermines expression of multiple genes involved in the TGFß/SMAD signaling pathway in Tregs including Activin. These findings suggest that YAP potentiates activity along a pro-Treg signaling axis. Overall design: The gene expression patterns in naïve T cells and nTregs from Wild type and YAP cKO (YAP flox/flox,CD4-Cre+) mice were assessed and compared using RNASeq. Sequencing was performed using a Illumina Hiseq2000.
Publication Title
YAP Is Essential for Treg-Mediated Suppression of Antitumor Immunity.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
AIMS/HYPOTHESIS: Manoeuvres aimed at increasing beta cell mass have been proposed as regenerative medicine strategies for diabetes treatment. Raf-1 kinase inhibitor protein 1 (RKIP1) is a common regulatory node of the mitogen-activated protein kinase (MAPK) and nuclear factor B (NF-B) pathways and therefore may be involved in regulation of beta cell homeostasis. The aim of this study was to investigate the involvement of RKIP1 in the control of beta cell mass and function.
Publication Title
The role of Raf-1 kinase inhibitor protein in the regulation of pancreatic beta cell proliferation in mice.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The emergence of immune resistance variants during immunotherapy is poorly understood. We generated a highly immune resistant cell line (P3) from a susceptible cell line (P0) by subjecting it to 3 rounds of in vivo immune selection. Subsequently, microarray analysis of P0 and P3 was performed to identify genes that may contribute to the increase in immune resistance.
Publication Title
Ectopic expression of vascular cell adhesion molecule-1 as a new mechanism for tumor immune evasion.
Sample Metadata Fields
No sample metadata fields
View Samples