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SRP035388
Drosophila melanogaster
6 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Background: RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously unknown exons are being reported. Initial reports of differences in exon usage, and splicing between samples as well as quantitative differences among samples are beginning to surface. Biological variation has been reported to be larger than technical variation. In addition, technical variation has been reported to be in line with expectations due to random sampling. However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript. Results: Independent Solexa/Illumina experiments containing technical replicates are analyzed. When coverage is low, large disagreements between technical replicates are apparent. Exon detection between technical replicates is highly variable when the coverage is less than 5 reads per nucleotide and estimates of gene expression are more likely to disagree when coverage is low. Although large disagreements in the estimates of expression are observed at all levels of coverage. Conclusions: Technical variability is too high to ignore. Technical variability results in inconsistent detection of exons at low levels of coverage. Further, the estimate of the relative abundance of a transcript can substantially disagree, even when coverage levels are high. This may be due to the low sampling fraction and if so, it will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads. We provide practical recommendations for dealing with the technical variability, without dramatic cost increases. Overall design: Three independent samples of D. melanogaster female heads were collected with each sample representing a unique pool of biological material. Each sample was prepared according to manufacturer's instructions and then the same library was run on two lanes of a Solexa/Illumina flow cell, resulting in two technical replicates for each biological replicate, runs were 36 base-pair paired end.
Publication Title
A flexible Bayesian method for detecting allelic imbalance in RNA-seq data.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 5 Downloadable Samples
- Illumina HiSeq 2500
Description
Genomic imprinting is an epigenetic phenomenon causing parental alleles to be active depending on their parent-of-origin. In plants, imprinted genes are mainly confined to the endosperm, an ephemeral tissue supporting embryo development. Differential methylation of histone H3 on lysine 27 (H3K27me3) established by the Polycomb Repressive Complex 2 (PRC2) is a major regulatory mechanism determining activity of paternally expressed imprinted genes (PEGs) in animals and plants. Here, we show that the coding region of many PEGs is marked by an epigenetic signature of H3K27me3, H3K9me2 and CHG methylation and that the combination of these three modifications correlates with paternally-biased gene expression in the endosperm. The maternal alleles of PEGs are marked by CHG methylation in the central cell, indicating that the repressive epigenetic signature of PEGs is established before fertilization. We use the presence of the three modifications to predict novel PEGs and propose that genomic imprinting is substantially more common than previously estimated based on expression data. Overall design: Col × Ler reciprocal crosses were performed using Arabidopsis lines expressing PHE1::NTF and PHE1::BirA. 4DAP siliques were collected and tissue homogenization and nuclei purification were performed from three biological replicates for LerxCol and two for ColxLer using INTACT. Total RNA was extracted from purified nuclei using the mirVana Isolation Kit Protocol (Ambion). mRNA extraction was performed using NEBNext Poly(A) mRNA Magnetic Isolation and the Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit from Illumina. Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.
Publication Title
Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mustela putorius furo
- 20 Downloadable Samples
Affymetrix Canine Genome 2.0 Array (canine2)
Description
Background: Type I interferons (IFNs) are essential to the clearance of viral diseases, in part by initiating upregulation of IFN regulated genes (IRGs). A clear distinction between genes upregulated directly by virus and genes upregulated by secondary IFN production has not been made. Here we investigated the genes regulated by IFN-a2b compared to the genes regulated by SARS-CoV infection in ferrets.
Publication Title
Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 65 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
The purpose of our study was to identify expression signatures and molecular markers associated with tumor recurrence and survival in patients with locally advanced head and neck squamous cell carcinoma (HNSCC).
Publication Title
Gene expression signatures and molecular markers associated with clinical outcome in locally advanced head and neck carcinoma.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mustela putorius furo
- 28 Downloadable Samples
- Affymetrix Canine Genome 2.0 Array (canine2)
Description
Background: Pandemic H1N1 influenza A is a newly emerging strain of human influenza that is easily transmitted between people and has spread globally to over 116 countries. Human infection leads to symptoms ranging from mild to severe with lower respiratory complications observed in a small but significant number of infected individuals. Little is currently known about host immunity and Pandemic H1N1 influenza infections.
Publication Title
Modeling host responses in ferrets during A/California/07/2009 influenza infection.
Sample Metadata Fields
Specimen part
View Samples- Mustela putorius furo
- 19 Downloadable Samples
- Illumina Genome Analyzer IIx, Illumina HiSeq 2000
Description
Ferrets were experimentaly infected with influenza A/California/07/2009. RNA samples from lungs and lymph nodes were analyzed by Illumina sequencing.
Publication Title
Sequencing, annotation, and characterization of the influenza ferret infectome.
Sample Metadata Fields
No sample metadata fields
View Samples- Mustela putorius furo
- 15 Downloadable Samples
- Affymetrix Canine Genome 2.0 Array (canine2)
Description
Pandemic H1N1 influenza A Human infection leads to symptoms ranging from mild to severe with lower respiratory complications observed in a small but significant number of infected individuals. Microarray analysis of the lymph nodes from ferrets infected with A/California/07/2009 shows intense gene upregulation during days 3 and 5 post-infection, and followed by marked downregulation during days 7 and 14 post infection. Gene expression profiles during the upregulation phase show intense chemokine activity, cell replication and activation of the lymphocyte-related signaling pathways.
Publication Title
Sequencing, annotation, and characterization of the influenza ferret infectome.
Sample Metadata Fields
Specimen part, Time
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Nitric oxide regulates plant development and responses to stress. However, the mechanisms underlying its regulatory role are still poorly known, and the impact of endogenous NO on the genome-wide transcriptome of plants has not been studied. For that purpose, we compared the transcriptomes of NO-deficient nia1nia2, noa1-2 and nia1nia2noa1-2 mutant versus wild type Arabidopsis thaliana plants. A core comprising 66 NO-responsive genes with similar expression in all NO-deficient genotypes was identified. Among them, 46 were down- and 20 up-regulated in NO-deficient plants, and thus positively and negatively regulated by endogenous NO, respectively. Accordingly with changes in its transcriptome, the NO-deficient nia1nia2noa1-2 mutant accumulated anthocyanins and indolic glucosinolates, displayed abnormal iron homeostasis in shoots and roots, and also showed altered root sensitivity to hormones such as ABA, ET, CYK and IAA. Together the presented data suggest NO functions essentially as a modulator of hormone action.
Publication Title
Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 40 Downloadable Samples
- Illumina human-6 v2.0 expression beadchip
Description
Critical disease caused by the new 2009 pandemic influenza virus (nvH1N1) is a challenge for physicians and scientist. As evidenced in SARS and H5N1, the development of an effective immune response plays a key role to overcome viral diseases. We studied host`s gene expression signatures, cytokine and antibody responses along the first week of hospitalization in 19 critically ill patients with primary nvH1N1 pneumonia and two degrees of respiratory involvement. Presence of comorbidities and absence of immunosuppresory conditions were the common antecedents in both groups. The most severe patients (n=12) showed persistant respiratory viral secretion, increased levels of pro-inflammatory cytokines and chemokines in serum, and elevated systemic levels of two immunosuppresory cytokines (IL-10 and IL-1ra). Both groups were able to produce specific antibodies against the virus. The average day for antibody production was day 9 in the course of the disease, defining an early period of innate immunity and a late period of adaptive immunity. The most severe group evidenced a poor expression of a set of MHC class II and T cell receptor (TCR) related genes participating in antigen presentation and cell mediated immune responses in the late phase. 7 patients of this group finally died. This findings evidence that, as observed in sepsis, severe H1N1 disease course with immunoparalysis, which could explain the poor control of the virus along with the increased incidence of bacterial superinfection observed in these patients.
Publication Title
Host adaptive immunity deficiency in severe pandemic influenza.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 763 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Affimetrix Human Gene 1.1 ST Array profiling of 763 primary medullobalstoma samples used for identification of Medullobastoma subtypes
Publication Title
Intertumoral Heterogeneity within Medulloblastoma Subgroups.
Sample Metadata Fields
Specimen part
View Samples