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Homo sapiens
2667 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
The development of the human brain is a complex and precisely regulated process that unfolds over a protracted period of time. Human-specific features of this process, especially the ways in which highly complex neural circuits of the cerebral cortex form, are likely to be important factors in the evolution of human specializations. However, in addition to giving us remarkable cognitive and motor abilities, the formation of intricate neural circuits may have also increased our susceptibility to psychiatric and neurodegenerative disorders. Furthermore, substantial evidence suggests that the symptoms and progression of many brain disorders are dramatically influenced by genetic and developmental processes that define regional cell phenotypes and connectivity. Sex differences also play an important role in brain development and function and are a risk factor for several brain disorders, such as autism spectrum disorders (ASD) and depression. Thus understanding the spatiotemporal dynamics and functional organization of the brain transcriptome is essential to teasing out the keys to human neurodevelopment, sexual dimorphism, and evolution as well as our increased susceptibility to certain brain disorders. Most transcriptome studies of the developing brain have been restricted to rodents, and those performed in humans and nonhuman primates have included relatively small sample sizes and predominantly focused on few regions or developmental time points. Because many prominent features of human brain development significantly diverge from those of well-characterized model organisms, the translation of knowledge across species is difficult, and it is likely that many underlying genetic processes have gone undetected. In this study, we have taken a genome-wide approach to analyze the human transcriptome at single-exon resolution with ~1.4 million exon-level probe sets in 16 brain regions from donors representing both sexes and multiple ethnicities, across pre and postnatal development, including adolescence, and adulthood. We also generated genome-wide genotype data for 2.5 million single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) for each specimen. Our analyses of the data revealed several features of the human brain transcriptome: spatiotemporal expression dynamics of individual and functionally related groups of genes, differential exon usage, sex-specific expression patterns and exon usage, and organization of the transcriptome into functional modules. We also profiled developmental trajectories of genes important for neurobiological themes and genes associated with ASD and schizophrenia. Finally, we present associations between specific SNPs and gene expression levels in different brain regions across development. The dataset presented here provides research opportunities and a wealth of information not previously available to the scientific community.
Publication Title
Spatio-temporal transcriptome of the human brain.
Sample Metadata Fields
Sex, Age
View Samples- Danio rerio
- 6 Downloadable Samples
IlluminaHiSeq2000
Description
Hydrogen peroxide is known to promote skin keratinocyte migration, although the mechanism of action is unclear. In an attempt to identify signaling pathways regulated by hydrogen peroxide in the skin, 3 day post fertilized (dpf) zebrafish larvae (nacre strain) were treated with 3mM hydrogen peroxide for 2 hours and subjected to RNA-seq analyses. Pools of about 1000 embryos for each of three biological replicates were derived from 5 independent mating pairs and raised to larval stages until 3 dpf. All larvae were subsequently homogenized in Trizol and total RNA was extracted using a chloroform extraction protocol treated with DNAse. Messenger RNA (mRNA) was subsequently purified from total RNA using biotin-tagged poly dT oligonucleotides and streptavidin-coated magnetic beads, followed by quality control using an Agilent Technologies 2100 Bioanalyzer (values >7 were used for sequencing). The poly(A)-tailed mRNA samples were fragmented and double-stranded cDNA generated by random priming for deep sequencing studies. Overall design: 6 samples total were analyzed. 3 untreated, and 3 hydrogen peroxide treated (3mM, 2hr)
Publication Title
Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Background: Cystic fibrosis (CF) is caused by mutations in the CFTR gene that impair function of this cAMP-regulated Cl- channel. In the small intestine, loss of CFTR function creates a dehydrated, acidic luminal environment which is believed to cause an accumulation of mucus, a phenotype characteristic of CF. CF mice have an innate immune response and impaired intestinal transit as well. We investigated whether lubiprostone, which activates the CLC2 Cl- channel, would improve the CF intestinal phenotype.
Publication Title
Lubiprostone ameliorates the cystic fibrosis mouse intestinal phenotype.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The expansion, trafficking and functional effectiveness of adoptively transferred CD8+ T-cells play a critical role in mediating effective anti-tumor immunity. However, the mechanisms which program the highly proliferative and functional state of CD8+ T-cells are not completely understood. We hypothesized that IL-12, a cytokine commonly induced by TLR activation, could enhance T-cell priming by altering responsiveness to antigen and cytokines. Priming of tumor specific CD8+ T-cells in the presence of IL-12 induced the acquisition of a 'polyfunctional' effector response and increased the generation of memory cells. Moreover, IL-12 priming also promoted high levels of the IL-2 receptor alpha-chain (CD25) and robust IL-2 mediated activation of STAT5. This sensitivity to IL-2 translated into enhanced in vivo proliferation of adoptively transferred CD8+ T-cells. Furthermore, real-time, in vivo imaging of T-cell trafficking confirmed the ability of IL-12 priming to drive in vivo proliferation. IL-12 priming enhanced the anti-tumor function of adoptively transferred cells by reducing established subcutaneous tumor burden, and significantly increasing survival in an established intracranial tumor model. Finally, IL-12 priming of human PBMCs generates tumor specific T-cells phenotypically and functionally similar to IL-12 primed Pmel-1 T-cells. These results highlight IL-12 as an important mediator of CD8+ T-cell effector function and anti-tumor immunity.
Publication Title
Enhanced sensitivity to IL-2 signaling regulates the clinical responsiveness of IL-12-primed CD8(+) T cells in a melanoma model.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Wild-type and exo mutant (SALK_098602) were grown in parallel in three independent experiments in a greenhouse. 3 x 2 profiles were established.
Publication Title
The extracellular EXO protein mediates cell expansion in Arabidopsis leaves.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Accumulating data indicate translation plays a role in cancer biology, particularly its rate limiting stage of initiation. Despite this evolving recognition, the function and importance of specific translation initiation factors is unresolved. The eukaryotic translation initiation complex eIF4F consists of eIF4E and eIF4G at a 1:1 ratio. Although it is expected that they display interdependent functions, several publications suggest independent mechanisms. This study is the first to directly assess the relative contribution of eIF4F components to the expressed cellular proteome, transcription factors, microRNAs, and phenotype in a malignancy known for extensive protein synthesis- multiple myeloma (MM). Previously, we have shown that eIF4E/eIF4GI attenuation (siRNA/ Avastin) deleteriously affected MM cells' fate and reduced levels of eIF4E/eIF4GI established targets. Here, we demonstrated that eIF4E/eIF4GI indeed have individual influences on cell proteome. We used an objective, high throughput assay of mRNA microarrays to examine the significance of eIF4E/eIF4GI silencing to several cellular facets such as transcription factors, microRNAs and phenotype. We showed different imprints for eIF4E and eIF4GI in all assayed aspects. These results promote our understanding of the relative contribution and importance of eIF4E and eIF4GI to the malignant phenotype and shed light on their function in eIF4F translation initiation complex.
Publication Title
eIF4E and eIF4GI have distinct and differential imprints on multiple myeloma's proteome and signaling.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples
GSE769- Mus musculus
- 6 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Total RNA was prepared using TRIzol reagent from the pancreata of eight week old male mice. The genotypes were Control: gastrin+/-, CFTR+/+; and CF: gastrin+/-, CFTR-/-. All mice were on 95% black6, 5% 129Sv background. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.
Publication Title
Acidic duodenal pH alters gene expression in the cystic fibrosis mouse pancreas.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina Genome Analyzer II
Description
The transition in developmental control from maternal to zygotic gene products marks a critical step in early embryogenesis. Here, we use GRO-seq analysis to map the genome-wide RNA polymerase distribution during the Drosophila maternal to zygotic transition. This analysis unambiguously identifies the zygotic transcriptome, and provides insight into its mechanisms of regulation. Overall design: Two replicates of GRO-seq at each time point.
Publication Title
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples- Homo sapiens
- 82 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
gene expression database and algorithm to define cell expression modules
Publication Title
Identifying gene expression modules that define human cell fates.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 55 Downloadable Samples
- IlluminaHiSeq2000
Description
Human neonates and older adults frequently exhibit a reduced capacity to control microbial infections. A variety of mechanisms involving both the innate and adaptive immune systems have been proposed to contribute to these deficiencies. The emergence of RNA sequencing (RNA-seq) as an accurate and quantitative method for examining mRNA levels provides an opportunity to compare transcriptional responses to a stimulus at a global scale in neonates, adults, and older adults. An examination of ex vivo monocyte responses to lipopolysaccharide stimulation or Listeria monocytogenes infection (with cord blood monocytes representing neonatal monocytes) revealed extensive similarities between all three age groups, with only a small number of genes exhibiting statistically significant differences. Using transcription factor motif analyses and RNA-seq data sets from a variety of mouse mutants, the most significant neonatal deficiencies corresponded to genes that require interferon response factor-3 or type 1 interferon signaling for their activation. In older adults, the most striking difference was broad, low-level activation of inflammatory genes prior to stimulation, consistent with prior evidence of a chronic inflammatory state in older adults. These results demonstrate the value of quantitative RNA-seq analyses and the feasibility of cross-species comparisons between well-defined mouse networks and human data sets. Overall design: RNA-seq of primary cells from three independent donors in three different age-groups across 3 time-points stimulated with either LPS or Listeria monocytogenes.
Publication Title
Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.
Sample Metadata Fields
No sample metadata fields
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