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Mus musculus
4 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Goal of this study was to compare transcriptional changes in CTL cells compared to Tc17 cells
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
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GSE9735- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Dataset of IL-12+IL-18 trated and Yersinia enterocolitica infected C57BL/6 NK cells
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 7 Downloadable Samples
IlluminaHiSeq2000
Description
Epstein-Barr virus (EBV) establishes lifelong infections in its human host. The virus is associated with a broad range of malignancies of lymphoid and epithelial origin, including Burkitt's lymphoma, post-transplant lymphoproliferative disease, nasopharyngeal carcinoma and gastric carcinoma. During the latent phase of its life cycle, EBV expresses more than 40 mature miRNAs that are highly abundant in tumor cells and may contribute to oncogenesis. Although multiple studies have assessed the relative expression profiles of EBV miRNAs in tumor cells, data linking these expression levels to functional target knockdown is mostly lacking. Therefore we set out to systematically assess the EBV miRNA expression levels in EBV+ tumour cell lines, and correlate this to their functional silencing capacity in these cells. We provide comprehensive EBV miRNA expression profiles of the EBV+ cell lines C666-1 (nasopharyngeal carcinoma), SNU-719 (gastric carcinoma), Jijoye (Burkitt's lymphoma), and AKBM (Burkitt's lymphoma) and of EBV- cells ectopically expressing the BART miRNA cluster. By deep sequencing the small RNA population and conducting miRNA-reporter experiments to assay miRNA potency, we were able to compare the expression profiles of the EBV miRNAs with their functional silencing efficacy. We observe a strong correlation between miRNA expression levels and functional miRNA activity. There is large variation in expression levels between EBV miRNAs in a given cell line, whereas the relative expression profiles are well maintained between cell lines. Furthermore, we show that miRNA arm selection bias is less pronounced for viral miRNAs than for human miRNAs. In addition to encoding the largest number of precursor miRNAs of all human herpesviruses, EBV expresses many miRNAs precursors that yield two functional miRNA strands, rather than one guide strand and a non-functional passenger strand. This reduced strand bias may increase the size of the EBV miRNA targetome.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Current methods to analyze gene expression measure steady-state levels of mRNA. In order to specifically analyze mRNA transcription, a technique has been developed that can be applied in-vivo. The technique is referred with the acronym NIAC-NTR (Non Invasive Application and Capture of Newly Transcribed RNA). This method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in-vivo. The method has been applied to a model of serum response of cultured primary mouse embryonic fibroblasts.
Publication Title
Microarray analysis of newly synthesized RNA in cells and animals.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Current methods to analyze gene expression measure steady-state levels of mRNA. In order to specifically analyze mRNA transcription, a technique has been developed that can be applied in-vivo in intact cells and animals. The technique is referred with the acronym NIAC-NTR (Non Invasive Application and Capture of Newly Transcribed RNA). This method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in-vivo. The method was applied to study renal ischemia reperfusion injury, demonstrating its applicability for whole organs in-vivo.
Publication Title
Microarray analysis of newly synthesized RNA in cells and animals.
Sample Metadata Fields
Age
View Samples GSE7363- Mus musculus
- 10 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Expression data from specific translational activity and cytoplasmic localization (nuclear retention) of mRNAs of primary mouse embryonic fibroblasts (MEF) early in response to serum.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 52 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In most organisms biological processes are partitioned, or phased to specific times over the day through interactions between external cycles of temperature (thermocycles) and light (photocycles), and the endogenous circadian clock. This orchestration of biological activities is achieved in part through an underlying transcriptional network. To understand how thermocycles, photocycles and the circadian clock interact to control time of day specific transcript abundance in Arabidopsis thaliana, we conducted four diurnal and three circadian two-day time courses using Affymetrix GeneChips (ATH1). All time courses were carried out with seven-day-old seedlings grown on agar plates under thermocycles (HC, hot/cold) and/or photocycles (LD, light/dark), or continuous conditions (LL, continuous light; DD, continuous dark, HH, continuous hot). Whole seedlings (50-100), including roots, stems and leaves were collected every four hours and frozen in liquid nitrogen. The four time courses interrogating the interaction between thermocycles, photocycles and the circadian clock were carried out as two four-day time courses. Four-day time courses were divided into two days under diurnal conditions, and two days under circadian conditions of continuous light and temperature. Thermocycles of 12 hours at 22C (hot) and 12 hours at 12C (cold) were used in this study. The two time courses interrogating photoperiod were conducted under short days (8 hrs light and 16 hrs dark) or long days (16 hrs light and 8 hrs dark) under constant temperature. In addition, the photoperiod time courses were in the Landsberg erecta (ler) accession, in contrast to the other time courses that are in the Columbia (col) background. The final time course interrogated circadian rhythmicity in seedlings grown completely in the dark (etiolated). Dark grown seedlings were synchronized with thermocycles, and plants were sampled under the circadian conditions of continuous dark and temperature.
Publication Title
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Sample Metadata Fields
Age, Time
View Samples- Arabidopsis thaliana
- 35 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis thaliana circadian and light signaling mutants have long hypocotyls under light/dark cycles. In order to determine if aberrant hypocotyl growth is due to time of day specific miss-expression of growth associated transcripts we conducted time course microarray experiments in the lux-2, lhy and phyB-9 mutants. The mutants and their parental genotypes were grown on plates under either intermediate days (12 hours light and 12 hours dark) for lux-2, or short day (8 hrs of light and 16 hrs of dark) for lhy and phyB-9, for seven days and tissue was collected every four hours over one day.
Publication Title
A circadian and light transcriptional network orchestrates plant growth
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina HiSeq 1500
Description
The goal was to characterize gene expression profiles of HSPCs in mice during Bordetella pertussis infection. Mice were immunized with acellular or whole cell pertussis vaccines. HSPCs were isolated by flow cytometric sorting and RNA was prepared for library prep and RNA seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 1500
Description
Total transcriptome analysis of naive or vaccinated murine lungs, post-challenge with Bordatella pertussis. Mice were immunized with PBS, whole cell pertussis vaccine, acellular pertussis vaccine, and RTX (adenylate cyclase toxoid) vaccine. The mice were then infected with B. pertussis and at 1 or 6/9 days post-challenge total lung RNA was purified for RNA-seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line, Treatment
View Samples