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Homo sapiens
47 Downloadable Samples
IlluminaHiSeq2500
Description
Transcriptome wide analysis of the skeletal muscle response to exercise in humans. Subjects performed one 60-min bout of moderate-intensity single-leg knee-extension exercise, and samples were obtained by biopsy of the vastus lateralis muscle before, immediately after, and at 3 hr post-exercise. Eight subjects were control (no drug), and eight received combined H1/H2-histamine receptor blockade prior to exercise. Overall design: Three time-points in each of 8 control and 8 histamine-blockade subjects. Time points are before exercise, immediately after exercise, and at 3 hrs post-exercise. Note: Alignments were re-run using an updated piece of software and the results are reported in PMID 29455450. The following supplementary files contain information on the differentially expressed genes that were identified by the new analysis of the data: GSE71972_Differential_Expression_Tables_Updated_20160830.xlsx GSE71972_Protein_Coding_Full_Counts_Updated_20160830.xlsx
Publication Title
A single dose of histamine-receptor antagonists before downhill running alters markers of muscle damage and delayed-onset muscle soreness.
Sample Metadata Fields
No sample metadata fields
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GSE2406- Arabidopsis thaliana
- 4 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Leaf transcriptome comparison of untransformed Col-0 Arabidopsis plants with plants transformed to be anti-sense for AtAOX1a (alternative oxidase). Two bio-replicates were sampled, for a total of four microarray chipsCol-0 and anti-sense leaf tissue from a first planting (samples GSM45208 and GSM45231, respectively), and from a second planting made one week later (samples GSM45209 and GSM45278, respectively). See sample descriptions for growth conditions and microarray procedure.
Publication Title
Characterization of transformed Arabidopsis with altered alternative oxidase levels and analysis of effects on reactive oxygen species in tissue.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 40 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Murine healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas.
Publication Title
Identification of early molecular markers for breast cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human healthy tissue samples, DCIS and invasive mammary tumors were analyzed in order to identify marker genes which show enhanced expresssion in DCIS and invasive ductal carcinomas.
Publication Title
Identification of early molecular markers for breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 51 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Differencies between groups between pre and post haematopoietic stem cell transplantation children
Publication Title
Genetic Background of Immune Complications after Allogeneic Hematopoietic Stem Cell Transplantation in Children.
Sample Metadata Fields
Specimen part, Disease stage
View Samples- Homo sapiens
- 32 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Differences between groups of children with obesity and healthy controls.
Publication Title
Looking for new diagnostic tools and biomarkers of hypertension in obese pediatric patients.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
O-GlcNAcylation is an essential, nutrient-sensitive post-translational modification, but its biochemical and phenotypic effects remain incompletely understood. To address this knowledge gap, we investigated the global transcriptional response to perturbations in O-GlcNAcylation. Unexpectedly, many transcriptional effects of O-GlcNAc transferase (OGT) inhibition were due to the activation of NRF2, the master regulator of redox stress tolerance. Moreover, we found that a signature of low OGT activity strongly correlates with NRF2 activation in multiple tumor expression datasets. Guided by this information, we identified KEAP1 (also known as KLHL19), the primary negative regulator of NRF2, as a direct substrate of OGT. We show that O-GlcNAcylation of KEAP1 at serine 104 is required for the efficient ubiquitination and degradation of NRF2. Interestingly, O-GlcNAc levels and NRF2 activation co-vary in response to glucose fluctuations, indicating that KEAP1 O-GlcNAcylation links nutrient sensing to downstream stress resistance. Our results reveal a novel regulatory connection between nutrient-sensitive glycosylation and NRF2 signaling, and provide a blueprint for future approaches to discover functionally important O-GlcNAcylation events on other KLHL family proteins in various experimental and disease contexts.
Publication Title
Glycosylation of KEAP1 links nutrient sensing to redox stress signaling.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- NextSeq 500
Description
Previous studies have reported that microglia depletion leads to impairment of synapse formation and these cells rapidly repopulate from CNS progenitors. However, the impact of microglia depletion and repopulation on the long-term state of the CNS environment has not been characterized. Here, we found by RNA-seq analysis that acute and synchronous microglia depletion results in a type 1-interferon inflammatory signature in degenerating somatosensory cortex in microglia-depleted mice. Transcriptomic and mass cytometry analysis of repopulated microglia demonstrates an interferon regulatory factor 7-driven activation state. Minocycline and anti-IFNAR1 antibody treatment attenuate the CNS type-1 interferon-driven inflammation and restore microglia homeostasis. Together, we found that acute microglia ablation induces a type-1 interferon activation state of grey matter microglia associated with acute neurodegeneration. Overall design: RNAseq analysis of brain cortical tissue from control and microglia-depleted mice.
Publication Title
Acute microglia ablation induces neurodegeneration in the somatosensory system.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
We identified genes whose expression changes between stage 8 and stage 10. We also identified genes whose expression was altered in stage 10 from temperature senstive ecdysone receptor mutant flies raised at the restrictive temperature. The experiments showed a significant number of genes that are upregulated in stage 10 depend EcR-mediated signaling. Overall design: 3 samples x 3 repeats
Publication Title
Steroid Signaling Establishes a Female Metabolic State and Regulates SREBP to Control Oocyte Lipid Accumulation.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Rattus norvegicus
- 24 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Analysis of expression changes in prelabeled laser-microdissected thoracic propriospinal neurons at different times after low-thoracic spinal cord transection in adult rats.
Publication Title
Intrinsic response of thoracic propriospinal neurons to axotomy.
Sample Metadata Fields
Sex, Age, Specimen part, Time
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