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SRP056889
Drosophila melanogaster
60 Downloadable Samples
Illumina HiSeq 2500
Description
CbtOE (Tim-gal4; UAS-cbtFLAG), Tim-gal4 (control for CbtOE), cbtRNAi (Tim-gal4-UAS-Dcr2-UAS-cbtIR-cbtE1) and Tim-gal4;UAS-Dcr2 (control for CbtRNAi) flies. Flies were entrained in LD (light: dark) condition for 3-4 days and harvested at six time points: ZT3, ZT7, ZT11, ZT15, ZT19, ZT23 Fly heads were collected, RNA was extracted and RNA-seq libraries were prepared as previously described (Engreitz et al., 2013) Overall design: Three samples of cbtRNAi and three samples of their controls. Two samples of cbtOE with two samples of their controls.
Publication Title
The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
Control (+/cbtE1-UAS-cbt RNAi) or cabut RNAi flies (Tim-gal4, UAS-cbt RNAi) were starved for 16 hours and then exposed to food containing different concentrations of sucrose: 0, 25, 50 and 100 % for 18 hours. Fly heads were collected, RNA was extracted and RNA-seq libraries were prepared as previously described (Engreitz et al., 2013) Overall design: For each sucrose concentration, two samples of cabut RNAi flies and one sample of control flies were sequenced.
Publication Title
The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Microarray data obtained from control, cbtRNAi (cabut RNAi), and cbtOE (cabut overexpression) flies. From each strain, fly heads at two different time points during the daynight cycle (ZT3 and ZT153) were collected.
Publication Title
The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Gallus gallus
- 29 Downloadable Samples
- Illumina HiSeq 2500
Description
Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus [lipopolysaccharide (LPS) or saline], and temperature (35°C or 25°C). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change = 2 and FDR = 0.05) in the broiler (N=283) than the Fayoumi (N=85), whereas heat treatment resulted in fewer DEG in broiler (N=22) compared to Fayoumi (N=107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat. The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens. Overall design: At 22 days of age, divergent chicken breeds (Fayoumi and broiler) were treated with a thermal treatment (heat stress at 35C, or thermoneutral at 25C as a control) for 3.5 hours, then stimulated subcutaneously with an inflammatory stimulus (LPS, or saline as a control) for another 3.5 hours. Chickens were euthanized and spleens were harvested. A total of 32 indivudally coded cDNA libraries were prepared using TruSeq v2 library preparation kit which selects for polyA mRNA. In this 2x2x2 full factorial design with the factors of breed, thermal treatment, and inflammatory stimulus, there were a total of 8 treatment groups. Each treatment group had a total of 4 animal biological replicates. Therefore, a total of 32 individual barcoded samples were sequenced. A total of 8 individually barcoded cDNA libraries were sequenced per lane using the HiSeq Illumina 2500, and we used 4 lanes total. Reads were mapped to Galgal 2.0.
Publication Title
Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat.
Sample Metadata Fields
Subject
View Samples- Gallus gallus
- 12 Downloadable Samples
- Illumina Genome Analyzer
Description
Background: Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression of genes to adapt the cell or organism to survive the heat challenge. RNA-seq technology allows rapid identification of environmentally responsive genes on a large scale. In this study, we have used RNA -seq to identify heat stress responsive genes in the chicken male white-leghorn hepat ocellular (LMH) cell line. Result: The transcripts of 812 genes were responsive to heat stress (p <0.01) with 235 genes up- regulated and 577 down-regulated following 2.5 hours of heat stress. Among the up- regulated were genes whose products function as chaperones, along with genes aff ecting collagen synthesis and deposition, transcription factors, chromatin remodelers and genes modulating the WNT and TGF-beta pathways. Predominant among the down-regulated genes were ones that affect DNA replication and repair along with chromosom al segregation. Many of the genes identified in this study have not been previously implicated in the heat stress response. Conclusion: These data extend our understanding of the transcriptome response to heat stress. Many of the identified biological processes and pathways likely function in adapting cells and organisms to hyperthermic stress. This study may provide important guides to future efforts attempting to improve species abilities to withstand heat stress through genome wide association studies and breeding. In addition, the genes down regulated by heat stress may provide important targets for improving hyperthemic treatment in cancer patients. Overall design: Cells were grown at either control ( 37oC) or heat stress (43oC) temperatures for 2.5 hours.
Publication Title
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Caenorhabditis elegans
- 20 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 20 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
Analysis of the transcriptional response to viral infection in C.elegans.
Publication Title
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Attempt to identify small non-coding RNAs that change in levels as a result of viral infection of C.elegans Overall design: Small non-coding RNA (18-30nt) was extracted from animals either infected with Orsay virus or uninfected as indicated.
Publication Title
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans.
Sample Metadata Fields
Cell line, Subject
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- Saccharomyces cerevisiae
- 24 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast cells were grown up in SD media containing all required amino acids. Each strain set was performed in triplicate. One set had no changes, the second set had 1mM methionine supplenting the media for the duration of growth and the third set was exposed to 0.5mM hydrogen peroxide for 15 minutes prior to harvesting
Publication Title
Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae.
Sample Metadata Fields
Compound
View Samples