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Gallus gallus
8 Downloadable Samples
Affymetrix Chicken Genome Array (chicken)
Description
Inner ear auditory and vestibular tissues differ in their responses to mechanical stimuli.
Publication Title
Distinct energy metabolism of auditory and vestibular sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
IlluminaHiSeq2000
Description
This experiment aims to identify the biological pathways and diseases associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells (PBMCs). Overall design: The experiment comprised of samples obtained from 3 healthy donors. The expression profiles of in vitro IL-13 stimulation were generated using RNA-seq technology for 3 PBMC samples at 24 hours. The transcriptional profiles of PBMCs without IL-13 stimulation were also generated to be used as controls. An IL-13R-alpha antagonist (Redpath et al. Biochemical Journal, 2013) was introduced into IL-13 stimulated PBMCs and the gene expression levels after 24h were profiled to examine the neutralization of IL-13 signaling by the antagonist.
Publication Title
Combining multiple tools outperforms individual methods in gene set enrichment analyses.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
We have developed a microfluidics-based in vitro model of the human gut allowing co-culture of human and microbial cells and subsequent multi-omic assessment of the effect of the co-culture on the host transcriptome.
Publication Title
A microfluidics-based in vitro model of the gastrointestinal human-microbe interface.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Despite accepted health benefits of dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic model, in which mice were colonized with a synthetic human gut microbiota, we elucidated the functional interactions between dietary fiber, the gut microbiota and the colonic mucus barrier, which serves as a primary defence against pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation promoted greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium, but only in the presence of a fiber-deprived microbiota that is pushed to degrade the mucus layer. Our work reveals intricate pathways linking diet, gut microbiome and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics.
Publication Title
A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 84 Downloadable Samples
- Illumina HiSeq 2500
Description
Database of gene expression in different haematopoietic cell types at haemosphere.org Overall design: Comparison of gene expression in different haematopoietic cell types
Publication Title
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
G-CSF is a hemopoietic growth factor that has a role in steady state granulopoiesis, as well as in mature neutrophil activation and function. We developed a neutralizing monoclonal antibody to the murine G-CSF receptor (G-CSFR), which antagonizes binding of murine G-CSF and inhibits G-CSFR signalling. Anti-G-CSFR rapidly halts the progression of established disease in collagen antibody-induced arthritis (CAbIA). Neutrophil accumulation in joints is inhibited, without rendering animals neutropenic, suggesting an effect on homing to inflammatory sites. Neutrophils in the blood and arthritic joints of anti-G-CSFR treated mice show alterations in cell adhesion receptors, while anti-G-CSFR suppresses local production of proinflammatory cytokines and chemokines known to drive tissue damage. Our aim in this study was to use differential gene expression analysis of joint and blood neutrophils to more thoroughly understand the effect of G-CSFR blockade on the inflammatory response following anti-G-CSFR therapy in CAbIA.
Publication Title
Therapeutic Targeting of the G-CSF Receptor Reduces Neutrophil Trafficking and Joint Inflammation in Antibody-Mediated Inflammatory Arthritis.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment
View Samples- Gallus gallus
- 12 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
A systematic survey of the transcriptional status of individual segments of the developing chick hindbrain (r1-5) and the adjacent region of the embryonic midbrain (m) during the HH11 stage of chick development
Publication Title
Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 21 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
C. elegans GLD-2 forms an active PAP with multiple RNA-binding partners to regulate diverse aspects of germline and early embryonic development. One GLD-2 partner, RNP-8, was previously shown to influence oocyte fate specification. To identify transcripts selectively associated with both GLD-2 and RNP-8, we employ a genomic approach using the method of RNA immunoprecipitation followed by microarray analysis (RIP-chip).
Publication Title
GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples
SRP189590- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-seq with male and female juvenile and adult spinal cords Overall design: RNA was isolated from 4 week and 8 week spinal cords for sequencing
Publication Title
Age and Sex-Related Changes to Gene Expression in the Mouse Spinal Cord.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Triticum aestivum
- 41 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Different wheat cultivars may be classified as either winter or spring varieties depending on whether they require exposure to an extended period of cold in order to become competent to flower. Using a growth regime that mimics the conditions that occur during a typical winter in Britain, we wished to survey the genes that are involved in phase transition as well as those involved in cold-acclimation.
Publication Title
Cold- and light-induced changes in the transcriptome of wheat leading to phase transition from vegetative to reproductive growth.
Sample Metadata Fields
No sample metadata fields
View Samples