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Homo sapiens
9 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The immortalized human urothelial cell line, UROtsa, was transformed in six parallel cultures with continual passaging in1 M Cd+2 until the cells were able to attain the ability to form colonies in soft agar and subcutaneous tumors in nude mice. The gene expression profiles between cadmium-transformed and control samples were compared and the differentially expressed genes were identified.
Publication Title
Variation of keratin 7 expression and other phenotypic characteristics of independent isolates of cadmium transformed human urothelial cells (UROtsa).
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Murine Genome U74A Array (mgu74a)
Description
Parkinson's disease pathogenesis proceeds through several phases, culminating in the loss of dopaminergic neurons of the substantia nigra (SN). Although the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of oxidative SN injury is frequently used to study degeneration of dopaminergic neurons in mice and non-human primates, an understanding of the temporal sequence of molecular events from inhibition of mitochondrial complex 1 to neuronal cell death is limited. Here, microarray analysis and integrative data mining were used to uncover pathways implicated in the progression of changes in dopaminergic neurons after MPTP administration. This approach enabled the identification of small, yet consistently significant, changes in gene expression within the SN of MPTP-treated animals. Such an analysis disclosed dysregulation of genes in three main areas related to neuronal function: cytoskeletal stability and maintenance, synaptic integrity, and cell cycle and apoptosis. The discovery and validation of these alterations provide molecular evidence for an evolving cascade of injury, dysfunction, and cell death.
Publication Title
Dysregulation of gene expression in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned mouse substantia nigra.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
Illumina HiSeq 2500, Illumina HiSeq 2000
Description
Relatively little is known about how the identity of early neuronal stem cells changes before and after neural tube closure (neurulation). We performed RNA sequencing on microdissected forebrain precursors and revealed sharp reductions in expresion of protein biosynthetic machinery after neurulation. These reductions were paralleled by down-regulation of Myc, which regulated forebrain precursor ribosome ribosome biogenesis. To study consequences of Myc dysregulation, we overexpressed Myc in Nestin+ neural progenitors, sorted these progenitors for RNA sequencing, and identified 135 genes that are differentially expressed between Myc-overexpressed embryos and their wildtype littermates. Overall design: The first RNA sequencing dataset contains micordissected neuroepithelium from E8.5 and E10.5 mouse embryos, two biological replicates for each age. The second RNA sequencing dataset contain FACS isolated Pax6+ neural progenitors form the cortex of E13.5 MYC-overexpressed embryos and their wildtype littermates, three biological replicates for each genotype.
Publication Title
Downregulation of ribosome biogenesis during early forebrain development.
Sample Metadata Fields
Specimen part, Cell line, Subject
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SRP049420- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
A diverse pool of RNAs remain encapsulated within the transcriptionally and translationally silent spermatozoon. These transcripts persist within the male gamete despite the dramatic reduction in cellular volume achieved through expulsion of the cytoplasm and quite possibly the nucleoplasm. The precise location of RNAs retained within the sperm cell remains largely unknown. However, early evidence suggested that many are embedded within the nucleus (1). To discern the global pattern of transcript compartmentalization in sperm, total RNA was extracted from whole mouse spermatozoa and detergent demembranated nuclei fractionated through a sucrose gradient. Isolated RNAs were subjected to RNA-sequencing (RNA-seq) and their abundance used to infer localization. Transcripts enriched in the unfractionated cells were related to the production and function of mitochondria and surprisingly, exosomes. The absence of these extracellular vesicles associated RNAs within the inner-nuclear compartment was suggestive of an origin other than sperm. This contributes to the growing evidence for sperm-bound exosomes rich in RNA. In comparison, the majority of the remaining sperm RNAs were associated with the nucleus. This included the abundant fragmented ribosomal transcripts which likely persist between the nuclear envelope and the perinuclear theca. The spermatozoal inner-nuclear compartment was also enriched in repetitive transcribed sequences. This included LINE elements and simple repeat sequences both of which have been shown to contribute to chromatin structure in other cell types suggesting that they may serve parallel roles in the spermatozoon. Overall design: RNA-seq analysis of whole mouse sperm and fractionated nuclei
Publication Title
The protein and transcript profiles of human semen.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Using cell-restricted transcriptome analysis, here we show that Drosophila ommatidial cone (or Semper) cells are enriched for conserved glial regulators and effectors, including many characteristic of vertebrate retinal glia: Müller glia and astrocytes. Overall design: RNA-seq based analysis of Drosophila retinal cone cells (3 developmental stages) and photoreceptors. 1 sample per cell type - 4 total libraries sequenced.
Publication Title
Multifunctional glial support by Semper cells in the Drosophila retina.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Neuronal function critically depends on coordinated subcellular distribution of mRNAs. Disturbed mRNA processing and axonal transport has been found in spinal muscular atrophy and could be causative for dysfunction and degeneration of motoneurons. Despite the advances made in characterizing the transport mechanisms of several axonal mRNAs, an unbiased approach to identify the axonal repertoire of mRNAs in healthy and degenerating motoneurons has been lacking. Here we used compartmentalized microfluidic chambers to investigate the somatodendritic and axonal mRNA content of cultured motoneurons by microarray analysis. In axons, transcripts related to protein synthesis and energy production were enriched relative to the somatodendritic compartment. Knockdown of Smn, the protein deficient in spinal muscular atrophy, produced a large number of transcript alterations in both compartments. Transcripts related to immune functions, including MHC class I genes, and with roles in RNA splicing were upregulated in the somatodendritic compartment. On the axonal side, transcripts associated with axon growth and synaptic activity were downregulated. These alterations provide evidence that subcellular localization of transcripts with axonal functions as well as regulation of specific transcripts with nonautonomous functions is disturbed in Smn-deficient motoneurons, most likely contributing to the pathophysiology of spinal muscular atrophy.
Publication Title
Subcellular transcriptome alterations in a cell culture model of spinal muscular atrophy point to widespread defects in axonal growth and presynaptic differentiation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
- IlluminaHiSeq2500
Description
RNA-Seq technique was applied to investigate the effects of four cDNA amplification kits and two RNA-Seq library preparation kits to the deep sequencing results at different perspectives. Overall design: The same set of semen samples were applied to investigate the qualitative and quantitative effect of four cDNA amplification methods and two RNA-Seq library preparation methods on sperm transcript profiling.
Publication Title
A comparison of sperm RNA-seq methods.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 13 Downloadable Samples
- Illumina HiSeq 2500
Description
Genomic imprinting is an allele-specific gene expression system important for mammalian development and function. The molecular basis of genomic imprinting is allele-specific DNA methylation 2. While it is well known that the de novo DNA methyltransferases Dnmt3a/b are responsible for the establishment of genomic imprinting, how the methylation mark is erased during primordial germ cell (PGC) reprogramming remains a mystery. Here we report that Tet1 plays a critical role in the erasure of genomic imprinting. We show that despite their identical genotype, progenies derived from mating between Tet1-KO males and wild-type females exhibit a number of variable phenotypes including placental, fetal and postnatal growth defects, and early embryonic lethality. These defects are, at least in part, caused by the dysregulation of imprinted genes, such as Peg10 and Peg3, which exhibit aberrant hypermethylation in the paternal allele of differential methylated regions (DMRs). RNA-seq reveals extensive dysregulation of imprinted genes in the next generation due to paternal functional loss of Tet1. Genome-wide DNA methylation analysis of E13.5 PGCs and sperm derived from Tet1-KO mice reveals hypermethylation of DMRs of imprinted genes in sperm, which can be traced back to PGCs. Dynamics of methylation change in Tet1-affected sites suggested that Tet1 swipes remaining methylation including imprinted genes at late reprogramming stage. We also revealed that Tet1play a role in paternal imprinting erasure in females germline. Thus, our study establishes a critical function for Tet1 in the erasure of genomic imprinting. Overall design: Gene expression analysis of E9.5 embryos
Publication Title
Role of Tet1 in erasure of genomic imprinting.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Mesenchymal stromal cells (MSCs) sense and modulate inflammation and represent potential clinical treatment for immune disorders. However, many details of the bidirectional interaction between MSCs and the innate immune comaprtment are still unsolved. Here we describe an unconventional but functional interaction between pro-inflammatory classically activated macrophages (M1M) and MSCs, with CD54 playing a central role. CD54 was upregulated and enriched specifically at the contact area between M1M and MSCs. Moreover, the specific interaction induced calcium signaling and increased the immunosuppressive capacities of MSCs dependent on CD54 mediation. Our data demonstrate that MSCs can detect an inflammatory microenvironment via a direct and physical interaction with innate immune cells. This finding opens new perspectives for MSC-based cell therapy.
Publication Title
CD54-Mediated Interaction with Pro-inflammatory Macrophages Increases the Immunosuppressive Function of Human Mesenchymal Stromal Cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Diet-induced obesity is reported to induce a phenotypic switch in adipose tissue macrophages from an antiinflammatory M2 state to a proinflammatory M1 state. Telmisartan, an angiotensin II type 1 receptor antagonist and a peroxisome proliferator-activated receptor-gamma (PPAR-gamma) agonist, reportedly has beneficial effects on insulin sensitivity. We studied the effects of telmisartan on the adipose tissue macrophage phenotype in high fat-fed mice. Telmisartan was administered for 5 weeks to high fat-fed C57BL/6 mice. Insulin sensitivity, macrophage infiltration, and the gene expressions of M1 and M2 markers in epididymal fat tissues were examined. Insulin- or a glucose-tolerance test showed that telmisartan treatment improved insulin resistance, decreasing the body weight gain, visceral fat weight and adipocyte size without affecting the amount of food intake. Telmisartan treatment reduced the number of CD11c-positive cells and crown-like structures. Telmisartan reduced the mRNA expressions of M1 macrophage markers, such as TNF-alpha and IL-6, and increased the expression of M2 markers, such as IL-10 and Mgl2. The reduction of M1 macrophage markers, as well as the increased gene expression of M2 markers especially IL-10, is a possible mechanism for the improvement of insulin sensitivity by telmisartan.
Publication Title
Telmisartan improves insulin resistance and modulates adipose tissue macrophage polarization in high-fat-fed mice.
Sample Metadata Fields
Sex, Specimen part, Treatment
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