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Drosophila melanogaster
45 Downloadable Samples
Illumina HiSeq 2000
Description
LNd, LNv, DN1 and TH neurons were manually sorted from dissociated Drosophila brains. RNA was extracted and transcriptomes analyzed via RNA-seq. Overall design: LNd, LNv, DN1 and TH neurons at various timepoints.
Publication Title
Striking circadian neuron diversity and cycling of <i>Drosophila</i> alternative splicing.
Sample Metadata Fields
Specimen part, Disease, Subject, Time
View Samples- Drosophila melanogaster
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrated a requirement of neuronal SOCE for Drosophila flight. We identified the early pupal stage to be critical and used RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. We down-regulated dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system for a 24h period during pupal development, and compared wild type and knockdown transcriptional profiles, immediately after knockdown as well as after a 36h recovery period. We found that dStim knockdown altered the expression of a number of genes. We also characterized one of the down-regulated genes, Ral for its role in flight. Thus, we identify neuronal SOCE as a mechanism that regulates expression of a number of genes during the development of the pupal nervous system. These genes can be further studied in the context of pupal nervous system development. Overall design: mRNA sequencing from two biological replicates each of wild type and dStim knockdown pupal brains at two time points - 36h APF (post 24h knockdown) and at 72h APF (Post knockdown and recovery)
Publication Title
A pupal transcriptomic screen identifies Ral as a target of store-operated calcium entry in Drosophila neurons.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 8 Downloadable Samples
- Illumina Genome Analyzer
Description
To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. 87% of introns assayed manifest more than 50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly, or slowly, with ~3% being almost completely retained in nascent pre-mRNA. Although individual introns showed slight but statistically significant differences in splicing efficiency, similar global levels of splicing were seen from both sources. Importantly, introns with low cotranscriptional splicing efficiencies are present in the same primary transcript with efficiently spliced introns, indicating that splicing is intron-specific. The analysis also indicates that cotranscriptional splicing is less efficient for first introns, longer introns and introns annotated as alternative. FinallyFinally, S2 cells expressing the slow RpII215C4 mutant manifest substantially less intron retention than wild-type S2 cells. Overall design: Examination of Total pA and Nascent RNA from 2 different cell populations and isolated fly heads.
Publication Title
Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Drosophila melanogaster
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
Neuroendocrine (NE) cells use large dense core vesicles (LDCVs) to traffic, process, store and secrete neuropeptide hormones through the regulated secretory pathway. The DIMM basic helix-loop-helix transcription factor of Drosophila controls the level of regulated secretory activity in NE cells. To pursue its mechanisms, we have performed two independent genome-wide analyses of DIMM's activities: (i) in vivo chromatin immunoprecipitation (ChIP) to define genomic sites of DIMM occupancy and (ii) deep sequencing of purified DIMM neurons to characterize their transcriptional profile. By this combined approach, we showed that DIMM binds to conserved E-boxes in enhancers of 212 genes whose expression is enriched in DIMM-expressing NE cells. DIMM binds preferentially to certain E-boxes within first introns of specific gene isoforms. Statistical machine learning revealed that flanking regions of putative DIMM binding sites contribute to its DNA binding specificity. DIMM's transcriptional repertoire features at least 20 LDCV constituents. In addition, DIMM notably targets the pro-secretory transcription factor, CREB-A, but significantly, DIMM does not target any neuropeptide genes. DIMM therefore prescribes the scale of secretory activity in NE neurons, by a systematic control of the regulated secretory pathway at steps that are both proximal and distal.
Publication Title
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.
Sample Metadata Fields
Sex, Specimen part
View Samples- Drosophila melanogaster
- 7 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
To amass candidate DIMM targets in addition to Phm (Park et al., 2008a), we used genome-wide microarray profiling by over-expressing DIMM throughout the embryonic nervous system. We compared profiles from experimental (elav>dimm) and control (elav-GAL4) embryos at 22-26 hr and 28-32 hr after egg laying (AEL). The design was intended to identify transcripts consistently up-regulated shortly after the induction of DIMM; in so doing, we could circumvent the lethality that ensues in late embryonic, and/ or by early larval stages, due to pan-neuronal DIMM expression.
Publication Title
Molecular organization of Drosophila neuroendocrine cells by Dimmed.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Post-translational modifications of proteins by Small Ubiquitin-like Modifiers (SUMOs) regulate protein degradation and localization, protein-protein interaction, and transcriptional activity. SUMO E3 ligase functions are executed by SIZ1/SIZ2 in yeast and PIAS family members in human. The Arabidopsis genome contains only one gene, SIZ1, that is orthologous to yeast SIZ1/SIZ2. Here, we show that the Arabidopsis SIZ1 interacts with SUM1 and SCE1a, the SUMO E2 conjugating enzyme. Compared to WT, the null mutant siz-1-3 is smaller in statue because of reduced expression of gene involved in brassinosteroid biosynthesis and signalling. Drought stress induces the accumulation of SUMO-protein conjugates, which is in part dependent on SIZ1 but not on ABA. Mutant plants of siz1-3 have significant lower tolerance to drought stress. Genome wide expression analysis identified about 2,000 Arabidopsis genes that are responsive to drought, and SIZ1 mediates the induction of 600 of these genes by a pathway independent of DREB2A and ABA. SIZ1-dependent, drought-responsive genes include those encoding enzymes of the anthocyanin synthesis pathway and jasmonate response. From these results, we conclude that SIZ1 regulates Arabidopsis development and plays a role in drought stress response probably through the control of gene expression.
Publication Title
The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses.
Sample Metadata Fields
Age
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Wild type Columbia and serrate-1 globular stage embryos were sequenced in order to profile miRNAs which are expressed in embryogenesis in Arabidopsis thaliana Overall design: Two biological replicates, two conditions
Publication Title
Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote.
Sample Metadata Fields
Specimen part, Subject
View Samples
GSE40348- Rattus norvegicus
- 300 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A novel transcriptomics based in vitro method to compare and predict hepatotoxicity based on mode of action.
Sample Metadata Fields
Sex, Time
View Samples- Rattus norvegicus
- 30 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
This study provides an evaluation of changes in gene expression associated with dioctyl phthalate treatment of rat hepatocytes in vitro.
Publication Title
A novel transcriptomics based in vitro method to compare and predict hepatotoxicity based on mode of action.
Sample Metadata Fields
Sex, Time
View Samples- Rattus norvegicus
- 30 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
This study provides an evaluation of changes in gene expression associated with acetominophen treatment of rat hepatocytes in vitro.
Publication Title
A novel transcriptomics based in vitro method to compare and predict hepatotoxicity based on mode of action.
Sample Metadata Fields
Sex, Time
View Samples