refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
    0
github link
Showing
of 191 results
Sort by

Filters

Technology

Platform

accession-icon GSE21663
Expression data from static and cyclic stretched porcine aortic heart valves
  • organism-icon Sus scrofa
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Porcine Genome Array (porcine)

Description

We explored the hypothesis that Serotonin (5HT) receptor signaling, that can be enhanced with 5HT transporter blockade with Fluoxetine (Fluox), in the aortic valve may vary based upon the biomechanical activity of the aortic valve leaflet.

Publication Title

Aortic valve cyclic stretch causes increased remodeling activity and enhanced serotonin receptor responsiveness.

Sample Metadata Fields

Specimen part, Disease, Treatment

View Samples
accession-icon GSE873
Muscle, normal extraocular, profile
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Molecular definition of human extraocular muscles (EOM). Human EOM were compared with limb (quadriceps femoris) muscle.

Publication Title

Definition of the unique human extraocular muscle allotype by expression profiling.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP152871
LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state [mouse]
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Deregulated activity of the LATS tumor suppressors has broad implications on cellular and tissue homeostasis. We examined the consequences of downregulation of either LATS1 or LATS2 in breast cancer. Consistent with their proposed tumor suppressive roles, expression of both paralogs is significantly downregulated in human breast cancer, and loss of either paralog accelerated mammary tumorigenesis in mice. However, each paralog had a distinct impact on breast cancer. Thus, LATS2 depletion in luminal B tumors resulted in metabolic rewiring, with increased glycolysis and reduced PPARg signaling. Furthermore, pharmacological activation of PPARg elicited LATS2-dependent death in luminal B-derived cells. In contrast, LATS1 depletion augmented cancer cell plasticity, skewing luminal B tumors towards increased expression of basal-like features, in association with increased resistance to hormone therapy. Hence, these two closely related paralogs play distinct roles in protection against breast cancer; tumors with reduced expression of either LATS1 or LATS2 may rewire signaling networks differently and thus respond differently to anti-cancer treatments. Overall design: RNA was isolated from Lats1-CKO and Lats2-CKO PyMT tumors (4 samples from each). For each genotype, the corresponding wt littermate controls were used (3 samples in each batch).

Publication Title

LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE33826
Gene expression in Plasmodium falciparum NF54 and P. falciparum HOX
  • organism-icon Plasmodium falciparum
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Plasmodium/Anopheles Genome Array (plasmodiumanopheles)

Description

P. falciparum NF54 proliferates under micro-aerophilic conditions in an environment of 3% O2, 4% CO2, 93% N2. This strain was gradually adapted to proliferate under standard tissue culture conditions of 5% CO2/95% air (~19% O2) to generate P. falciparum HOX. We compared global gene expression profiles of the two strains to identify differences, if any.

Publication Title

Model system to define pharmacokinetic requirements for antimalarial drug efficacy.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE19156
Air-liquid interfacial biofilm vs planktonic S. cerevisiae cells
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

Goal was to identify yeast genes whose expression changed as a function of the shift from growth in bulk culture to growth in an air-liquid interfacial biofilm.

Publication Title

Ethanol-independent biofilm formation by a flor wine yeast strain of Saccharomyces cerevisiae.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE9951
Transcriptome analyses in normal prostate epithelial cells following exposure to low-dose cadmium
  • organism-icon Homo sapiens
  • sample-icon 19 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

BACKGROUND: Cadmium is implicated in prostate carcinogenesis, but its oncogenic action remains unclear.

Publication Title

Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor.

Sample Metadata Fields

Sex

View Samples
accession-icon GSE58771
Expression data from Arabidopsis thaliana root and piriformaspora indica during log and short term interaction
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant per-formance, growth and resistance/tolerance against abiotic and biotic stress. We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the gene expression pattern indicates a shift from defense to mutualistic interaction.

Publication Title

The interaction of Arabidopsis with Piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of the two symbionts.

Sample Metadata Fields

Age, Specimen part

View Samples
accession-icon GSE44561
Effect of Notch1 pathway activation on high-grade glioma cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.1 ST Array (hugene11st)

Description

In this study, we explored the transcriptomic consequences of strong activation of the Notch pathway in embryonic human neural stem cells and in gliomas. For this we used a forced expression of the Notch intracellular domain (NICD).

Publication Title

Notch1 stimulation induces a vascularization switch with pericyte-like cell differentiation of glioblastoma stem cells.

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE3307
Comparative profiling in 13 muscle disease groups
  • organism-icon Homo sapiens
  • sample-icon 235 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Summary: Genetic disorders of muscle cause muscular dystrophy, and are some of the most common inborn errors of metabolism. Muscle also rapidly remodels in response to training and innervation. Muscle weakness and wasting is important in such conditions as aging, critical care medicine, space flight, and diabetes. Finally, muscle can also be used to investigate systemic defects, and the compensatory mechansisms invoked by cells to overcome biochemical and genetic abnormalities. Here, we provide a 13 group data set for comparative profiling of human skeletal muscle. Groups studied are: Normal human skeletal muscle, Acute quadriplegic myopathy (AQM; critical care myopathy), Juvenile dermatomyositis (JDM), Amyotophic lateral sclerosis (ALS), spastic paraplegia (SPG4; spastin), Fascioscapulohumeral muscular dystrophy (FSHD), Emery Dreifuss muscular dystrophy (both X linked recessive emerin form; autosomal dominant Lamin A/C form), Becker muscular dystrophy (partial loss of dystrophin), Duchenne muscular dystrophy (complete loss of dystrophin), Calpain 3 (LGMD2A), dysferlin (LGMD2B), FKRP (glycosylation defect; homozygous for a missense mutation). U133A and U133B microarrays are both available.

Publication Title

Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration.

Sample Metadata Fields

Specimen part, Disease, Disease stage

View Samples
accession-icon GSE29670
Polymicrobial periodontal pathogens transcriptomes in calvarial bone and soft tissue
  • organism-icon Mus musculus
  • sample-icon 19 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

The objectives of this investigation were to examine changes in the host transcriptional profiles during a polymicrobial periodontal pathogens Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia infection using a murine calvarial model of inflammation and bone resorption. P. gingivalis FDC 381, T. denticola ATCC 35404, and T. forsythia ATCC 43037 was injected into the subcutaneous soft tissue over the calvaria of BALB/c mice for 3 days, after which the soft tissues and calvarial bones were excised. RNA was isolated from infected soft tissues and calvarial bones and analyzed for transcript profiles using Murine GeneChip MG-MOE430A Affymetrix arrays to provide a molecular profile of the events that occur following infection of these tissues.

Publication Title

Polymicrobial periodontal pathogen transcriptomes in calvarial bone and soft tissue.

Sample Metadata Fields

Age, Specimen part

View Samples
...

refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

Powered by Alex's Lemonade Stand Foundation

Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

BSD 3-Clause LicensePrivacyTerms of UseContact