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Xenopus laevis
31 Downloadable Samples
Affymetrix Xenopus laevis Genome Array (xenopuslaevis)
Description
A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here we used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators as well as over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodals, Mixer and Sox17 have both shared and distinct sets of downstream targets and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, Sox17 and Bix1, 2, 4 and between Sox17 and Xnr4. We find that Mixer does not function primarily via Sox17 as previously proposed. This data provides a new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network.
Publication Title
Global analysis of the transcriptional network controlling Xenopus endoderm formation.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 8 Downloadable Samples
Illumina Genome Analyzer IIx, Illumina HiSeq 2000
Description
mRNA sequencing was used to identify genome wide transcriptional changes occuring in fly heads in response to spermidine feeding. This study shed light on the molecular mechanisms through wich spermidine can protect against age-dependent memory impairment. Overall design: mRNA profiles from 3 and 10 day old Drosophila melanogaster heads were generated in duplicate by deep sequencing using Illumina GAIIx. mRNA profiles from flies that were fed food with 5mM spermidine were compared to profiles from flies that had no spermidine in thier food.
Publication Title
Restoring polyamines protects from age-induced memory impairment in an autophagy-dependent manner.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2000
Description
Around 20-25% of childhood acute lymphoblastic leukemias carry the TEL-AML1 (TA) fusion gene. It is a fusion of two central hematopoietic transcription factors, TEL (ETV6) and AML1 (RUNX1). Despite its prevalence, the exact genomic targets of TA have remained elusive. We evaluated gene loci and enhancers targeted by TA genome-wide in precursor B acute leukemia cells using global nuclear run-on sequencing (GRO-seq). Overall design: Nascent RNA expression profiles were generated with GRO-seq after TEL-AML1 expression in the Nalm6 pre-B-ALL cell line in four different time points (0, 4, 12 and 24 h). TEL-AML1-mut and luciferase induction cell lines were used as controls. Two replicates were included for all six samples.
Publication Title
Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Interferon-γ Inhibits Ebola Virus Infection.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Episodic Ebola virus (EBOV) outbreaks, such as the current one in West Africa, emphasize the critical need for novel antivirals against this highly pathogenic virus. Here, we demonstrate that interferon gamma (IFN) prevents morbidity and mortality associated with EBOV infection when administered to mice either 24 hours prior to or 2 hours following EBOV infection. Microarray studies with IFN-stimulated human macrophages identified novel interferon-stimulated genes (ISGs) that inhibit EBOV infection upon ectopic expression. IFN treatment reduced viral RNA levels in macrophages to a similar degree as cells treated with the protein synthesis inhibitor, cycloheximide, suggesting that IFN treatment inhibits genome replication. As IFN treatment robustly protects mice against EBOV infection, we propose that this FDA-approved drug may serve as a useful prophylactic or therapeutic strategy during EBOV outbreaks, contributing to the currently limited arsenal of filovirus antivirals.
Publication Title
Interferon-γ Inhibits Ebola Virus Infection.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Episodic Ebola virus (EBOV) outbreaks, such as the current one in West Africa, emphasize the critical need for novel antivirals against this highly pathogenic virus. Here, we demonstrate that interferon gamma (IFN) prevents morbidity and mortality associated with EBOV infection when administered to mice either 24 hours prior to or 2 hours following EBOV infection. Microarray studies with IFN-stimulated human macrophages identified novel interferon-stimulated genes (ISGs) that inhibit EBOV infection upon ectopic expression. IFN treatment reduced viral RNA levels in macrophages to a similar degree as cells treated with the protein synthesis inhibitor, cycloheximide, suggesting that IFN treatment inhibits genome replication. As IFN treatment robustly protects mice against EBOV infection, we propose that this FDA-approved drug may serve as a useful prophylactic or therapeutic strategy during EBOV outbreaks, contributing to the currently limited arsenal of filovirus antivirals.
Publication Title
Interferon-γ Inhibits Ebola Virus Infection.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
We report here that human mitochondria contain small RNA including microRNA, piRNA, tRNA, rRNA, and RNA repeats. Mitochondria from human cells were purified and RNA isolated. Small RNAs were purified, library generated and analyzed by Illumina Hiseq 2000 system. The sequencing generated 19.5 and 17.7 million reads from HEK-293 and HeLa respectively. 91% and 97% sequences of HEK293 and HeLa respectively were annotated to various classes of small RNA. The total percentage of 4.21 and 2.58 sequences from HEK293 and HeLa respectively was found to be of miRNA. Further, we found only 1.2 % sequences from both the libraries aligned to mitochondrial genome. These results suggest that there is efficient transport of nuclear encoded small RNA to mitochondria. The small RNA in mitochondria may regulate critical cellular processes. Overall design: Analyzing the smallRNA in human mitochondria from two human cell lines (HEK-293 and HeLa).
Publication Title
Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Oryza sativa indica group
- 16 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. The number of differentially expressed genes was drastically reduced to 70 and 30, by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents.
Publication Title
Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).
Sample Metadata Fields
No sample metadata fields
View Samples
E-MTAB-912- Saccharomyces cerevisiae
- 4 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Administration of spermidine, a natural polyamine whose intracellular concentration declines during human ageing, markedly extends the lifespan of various model organisms including yeast, flies and worms. In ageing yeast, spermidine treatment triggeres epigenetic deacetylation of histone H3 through inhibition of histone acetyltransferases (HAT), leading to induction of autophagy and thereby suppressing oxidative stress and necrosis. In order to further characterize the effects by spermidine supplementation of aging yeast cultures and to understand how global histone deacetylation affects gene transcription during aging, Affymetrix-based microarray analyses of three day old as well as ten day old cultures with and without administration of spermidine was performed.
Publication Title
Induction of autophagy by spermidine promotes longevity.
Sample Metadata Fields
Age, Compound, Time
View Samples GSE27568- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Analysis of Ubb knockout mouse testes at 7, 4, 21, and 28 dpp. Ubiquitin (Ub) is an essential protein found in all eukaryotic cells and plays important roles in a variety of cellular functions including germ cell development. Targeted disruption of the polyubiquitin gene Ubb results in male and female infertility in mice with germ cells arrested at meiotic prophase I.
Publication Title
Altered testicular gene expression patterns in mice lacking the polyubiquitin gene Ubb.
Sample Metadata Fields
Specimen part
View Samples