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E-AFMX-1
Macaca mulatta, Mus caroli, Mus musculus, Pan troglodytes, Pongo pygmaeus, Homo sapiens, Mus spretus
13 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.
Publication Title
A neutral model of transcriptome evolution.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Pan troglodytes, Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U95B Array (hgu95b), Affymetrix Human Genome U95D Array (hgu95d), Affymetrix Human Genome U95 Version 2 Array (hgu95av2), Affymetrix Human Genome U95C Array (hgu95c), Affymetrix Human Genome U95E Array (hgu95e)
Description
Gene expression profiling in brain of three adult humans and three adult chimpanzees
Publication Title
DNA sequence and comparative analysis of chimpanzee chromosome 22.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Drosophila melanogaster
- 45 Downloadable Samples
Illumina HiSeq 2500
Description
Test effects of mtDNA variation on nuclear transcript expression using various mtDNA haplotypes on isogenic nuclear backgrounds
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 28 Downloadable Samples
- Illumina HiSeq 2000
Description
Arabidopsis thaliana is a main model species for plant science, especially for such branches as molecular biology, genetics and genomics. We present here first genome-wide analysis of expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing (RNA-seq). To determine whether the developmental map represented the majority of the expressed genes, we analyzed gene expression under various abiotic stress conditions.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 26 Downloadable Samples
- Illumina HiSeq 2000
Description
Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been described. In this study we analyzed gene expression during Arabidopsis thaliana meristem development from day 7 to 16 after germination in one-day increments. The dynamics of the expression of the main flowering regulators were consistent with previous reports: notably, the expression of FLOWERING LOCUS C (FLC) decreased over the course of the time series while expression of LEAFY (LFY) increased. This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. GO enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle, suggesting that during transition to the flowering stage a change in dynamics of cell division takes place. In particular, we hypothesize that a subset of the meristematic cells experiences a forced exit from G0 at day 10. Finally, we observed an acceleration of the cell cycle at day 11, which may be linked to meristem reorganization preceding activation of LFY.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Drosophila melanogaster
- 23 Downloadable Samples
- Illumina HiSeq 2000
Description
Mitonuclear transcriptomics
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 12 Downloadable Samples
- IlluminaHiSeq2000
Description
Human cell line HCT116 incubated with Myxothiazol for 5 or 17 hours
Publication Title
A sustained deficiency of mitochondrial respiratory complex III induces an apoptotic cell death through the p53-mediated inhibition of pro-survival activities of the activating transcription factor 4.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
- Illumina HiSeq 4000
Description
We sequenced DGRP (Drosophila Genetic Reference Panel) line 208 for strand-specific RNA-seq in head, testis and ovary. The RNA-seq (2x150bp) data is intended to investigate the expression profiles of polymorphic duplications and de novo gene, as well as other lncRNAs.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-Seq of EBV-positive B-lymphoblastoid cell line MP1 and EBV-positive Burkitt’s lymphoma cell line Raji
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Danio rerio
- 82 Downloadable Samples
- Illumina HiSeq 2000
Description
Post-transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal-to-Zygotic Transition (MZT), thousands of maternal transcripts are regulated, however, how different cis-elements and trans-factors are integrated to determine mRNA stability is still poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3'-UTR, including poly-U motifs that are associated with mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA-protein interactions and found that poly-U binding proteins are preferentially associated with 3'-UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly-C motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA-seq timecourse part of the study.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples