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SRP094023
Mus musculus
32 Downloadable Samples
NextSeq 500
Description
We report that hippocampal neuronal pentraxin 2 (Nptx2) plays an important role in mediating anxiety. To better understand the mechanism of how Nptx2 alters anxiety, we detected the differential hippocampal gene expression between Nptx2 WT and KO. To do so, we took Nptx2 WT and KO (n = 3) mice for RNA-sequencing (RNAseq)
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 14 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Huh7/5-2 cells (Binder et al., Hepatology 2007) were mock infected (DMEM) (time points 4 and 48 h) or infected with the chimeric HCV virus Jc1 (Pietschmann et al., PNAS 2006) (all time points).
Publication Title
Viral immune modulators perturb the human molecular network by common and unique strategies.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 4000
Description
Brown adipose tissue (BAT) is specialized for UCP1-dependent uncoupled thermogenesis. BAT is not thermogenic under an unstimulated state; whereas can be quickly activated to generate heat after sympathetic activation. CL316,243 is a specific agonist of beta3 adrenergic receptor on brown adipocytes. Treatment of CL316,243 in mice leads to potent and specific activation of BAT. The goal of this project is to characterize acute gene expression alterations in the early stage of BAT thermogenic activation.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Dysregulated inflammation is implicated in the pathobiology of aging, yet platelet-leukocyte interactions and downstream inflammatory gene synthesis in older adults remains poorly understood. Highly-purified human platelets and monocytes were isolated from healthy younger (age<45, n=37) and older (age60, n=30) adults and incubated together under autologous and non-autologous conditions. Inflammatory gene synthesis by monocytes, basally and in the presence of platelets, was examined. Next-generation RNA-sequencing allowed for unbiased profiling of the platelet transcriptome in aging. Basal IL-8 and MCP-1 synthesis by monocytes alone did not differ between older and younger adults. However, in the presence of autologous platelets, monocytes from older adults synthesized greater IL-8 (415 vs. 92 ng/mL, p<0.0001) and MCP-1 (867150 vs. 21636 ng/mL, p<0.0001) than younger adults. Non-autologous experiments demonstrated that platelets from older adults were sufficient for upregulating inflammatory gene synthesis by monocytes. Using RNA-seq followed by validation via RT-PCR and immunoblot, we discovered that granzyme A (GrmA), a serine protease not previously identified in human platelets, is increased in aging (~9-fold vs. younger adults, p<0.05) and governs increased IL-8 and MCP-1 synthesis through TLR4 and caspase-1. Inhibiting GrmA reduced the excessive IL-8 and MCP-1 synthesis in older adults to levels similar to younger adults. In summary, human aging is associated with changes in the platelet transcriptome and proteome. GrmA is present and bioactive in human platelets, is higher in older adults, and controls inflammatory gene synthesis by monocytes. Alterations in the platelet molecular signature and downstream signaling to monocytes may contribute to dysregulated inflammatory syndromes and adverse outcomes in older adults.
Publication Title
Granzyme A in Human Platelets Regulates the Synthesis of Proinflammatory Cytokines by Monocytes in Aging.
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Homo sapiens
- 38 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
Gene expression analyis of two neonatal fibroblasts (BJ and HFF1), one adult dermal fibroblasts (NFH2), two BJ-derived human iPSCs (iB4 and iB5), two HFF1-derived iPSCs (iPS 2 and iPS4), four NFH2-derived iPSCs (OiPS3, OiPS6, OiPS8, OiPS16), one amniotic fluid cells and three derived iPSCs (lines 4, 5, 6, 10, and 41), two human ES cells (H1 and H9), neonatal fibroblasts transduced with the four retroviral factors (OKSM) after 24h, 48h, and 72h, neonatal fibroblasts treated with EDHB for 24h, 48h, and 72h, neonatal fibroblasts transduced with four factors and treated with EDHB for 24h, 48h, and 72h, neonatal fibroblasts knocked down for HIF1A (HIF1-KD) and for a scrambled sequence (SCR-KD)
Publication Title
HIF1α modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1-3 and PKM2.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Cell line
View Samples- Mus musculus
- 26 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part
View Samples- Rattus norvegicus
- 42 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
During kidney development segmented epithelia of the nephron derive from progenitor cells in the metanephric mesenchyme after induction by secreted molecules from the ureteric bud. We have identified three distinct inductive activities from a ureteric bud cell line. These include leukemia inhibitory factor (LIF), neutrophil gelatinase-associated lipocalin (NGAL) and an active fraction currently referred to as ANX. Each of these activities induces segmented nephron epithelia in isolated rat metanephric mesenchyme over a time period of 7 days. This study was designed to characterize the temporal sequence of gene expression in the course of the conversion process induced by each of the distinct inducers.
Publication Title
beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors.
Alternate Accession IDs
Sample Metadata Fields
Time
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Analysis of genes regulated by Gab1 mediated signaling in hair cycle initiation
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Malignant Hodgkin's lymphoma (HL) cells are characterized by constitutive activation of the canonical as well as the non-canonical NF-B signaling cascades. We depleted subunit combinations corresponding to either canonical (p50/RelA) or non-canonical (p52/RelB) dimers in the HL cell line L-1236 and performed Affymetrix microarray analysis. Knockdown of p52/RelB affected the expression of a significantly higher number of genes than the knockdown of p50/RelA. The two sets of target genes presented a partial overlap, however they also revealed specific genes that are involved in distinct aspects of tumor biology.
Publication Title
A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 24 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Shp2 signaling suppresses senescence in PyMT-induced mammary gland cancer in mice.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples