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E-MEXP-347
Mus musculus
24 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a)
Description
Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice.
Publication Title
Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 74 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We investigated the differential regulation patterns of type I anti-CD20 monoclonal antibody (mAb) rituximab and type II obinutuzumab on a transcriptional level. Using a panel of MCL cell lines, we determined the effects of obinutuzumab and rituximab as monotherapies as well as in combination on cell viability and proliferation.
Publication Title
Differential regulation patterns of the anti-CD20 antibodies obinutuzumab and rituximab in mantle cell lymphoma.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Rattus norvegicus
- 69 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Seven novel and potent Raf small molecule kinase inhibitors were evaluated in 7-day oral repeat-dose rat toxicity studies. All compounds tested induced hyperplasia in multiple tissues. Microarrays were used to investigate transciptional changes associated by treatment with a single compound to gain insight into the cellular changes that may contribute to the tissue hyperplasia.
Publication Title
Raf inhibition causes extensive multiple tissue hyperplasia and urinary bladder neoplasia in the rat.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Rattus norvegicus
- 50 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Fetal asphyctic (FA) preconditioning is effective in attenuating brain damage incurred by a subsequent perinatal asphyctic insult. Unraveling mechanisms of this endogenous neuroprotection, activated by FA preconditioning, is an important step towards new clinical strategies for asphyctic neonates. Genomic reprogramming is thought to be, at least in part, responsible for the protective effect of preconditioning. Therefore, we investigated whole genome differential expression in the preconditioned rat brain.
Publication Title
Fetal asphyctic preconditioning alters the transcriptional response to perinatal asphyxia.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Transcriptome analysis of partially degraded and fragmented RNA samples from body fluids
Publication Title
Exon-level expression profiling: a comprehensive transcriptome analysis of oral fluids.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina HiSeq 4000
Description
TRAP-seq gene expression profiling. GFP-L10a is expressed in BDNF+ or PACAP+ in preoptic area. Bdnf+ or Pacap+ cells in the preoptic area are labelled with GFP-L10a fusion protein expression to study cell-type specific gene expression. We used adult BDNF-Cre (custom generated, discussed in submitted paper) and Pacap-Cre mice (Allen Brain Institute, gift Hongkui Zeng) and injected Cre-depndent adenoassociated virus (AAV2-EF1a-DIO-EGFP-L10a, custom made) into the ventromedial preoptic area. Overall design: Comparison of Immunoprecipitation and Input fraction mRNA
Publication Title
Warm-Sensitive Neurons that Control Body Temperature.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The eosinophil transcriptome analysis indicated a robust transcription change in eosinophils following allergen challenge in the lung.
Publication Title
Carbonic anhydrase IV is expressed on IL-5-activated murine eosinophils.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-Seq profiling identifies transcripts enriched in preoptic neurons activated by warm temperature challenge Overall design: Animals are subject to warm temperatures during which ribosomal S6 protein is phosphorylated selectively in active neurons. Transcripts associated with phosphorylated ribosome is isolated by immunoprecipitation. Comparison of Immunoprecipitation and Input fraction mRNA
Publication Title
Warm-Sensitive Neurons that Control Body Temperature.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 29 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
To gain insight into the dynamic molecular processes that are altered during prolonged wakefulness and during sleep. We performed an RNA expression profiling study examining temporal changes in the brain of Drosophila in relationship to the duration of prior sleep or wakefulness. Our experimental design allowed us to determine whether genes identified as differentially regulated between sleep and wakefulness were up- or down-regulated in these states.
Publication Title
Multiple mechanisms limit the duration of wakefulness in Drosophila brain.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Danio rerio
- 6 Downloadable Samples
- NextSeq 500
Description
The SWI/SNF-family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas, gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells, while it also affects Polycomb repressive complex 2 (PRC2) silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis, we knocked out atrx in our previously published p53/nf1-deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. Complete inactivation of atrx using CRISPR-cas9 was lethal in developing fish and resulted in an alpha-thalassemia-like phenotype including reduced alpha-globin expression. In p53/nf1-deficient zebrafish neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/- fish, but these fish developed various tumors that were not observed in their atrx+/+ siblings, including epithelioid sarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma and rare types of carcinoma. Most of these cancer types are included in the AACR Genie database of human tumors associated with mutant ATRX, indicating that our zebrafish model reliably reflects a role for ATRX-loss in the early pathogenesis of these types of human cancers. RNA-seq of p53/nf1- and p53/nf1/atrx-deficient tumors revealed that down-regulation of telomerase accompanied ALT-mediated lengthening of the telomeres in atrx-mutant samples. Moreover, inactivating mutations in atrx disturbed PRC2-target gene silencing, indicating a connection between ATRX loss and PRC2 dysfunction in cancer development. Overall design: Gene expression values were derived from paired end RNA-Seq data that compared zebrafish samples from p53/nf1/atrx-deficient tumors to samples from atrx-wildtype controls (3 vs. 3 samples).
Publication Title
Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies.
Sample Metadata Fields
Subject
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