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SRP165993
Danio rerio
7 Downloadable Samples
Illumina HiSeq 2500
Description
We compared transcriptomes of two ependymoglial populations isolated from adult zebrafish telencephalon. Overall design: Ependymoglial cells are acutely isolated from the adult zebrafish brains form 3 months old transgenic gfap:GFP animals. GFP is experssed in all ependymoglial cells and two populations are separated using GFP intensity in FACS.
Publication Title
The Aryl Hydrocarbon Receptor Pathway Defines the Time Frame for Restorative Neurogenesis.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 24 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
The Drosophila phagocytic receptor Eater is expressed specifically in phagocytic hemocytes. It contributes to host immune defense and is required for survival of bacterial infections. Eater is involved in recognition and phagocytosis of bacteria.
Publication Title
Phagocytosis of bacterial pathogens.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mutations in the inner nuclear membrane protein emerin cause muscular dystrophy. Current evidence suggests that the muscle wasting is related to defects in muscle progenitor cell differentiation and regeneration. We obtained miRNA and mRNA expression data from wildtype and emerin-null cells and looked at gene expression differences between them.
Publication Title
Loss of emerin alters myogenic signaling and miRNA expression in mouse myogenic progenitors.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 34 Downloadable Samples
- Illumina HiScanSQ
Description
RNA sequencing was performed on proliferating and differentiating wildtype and emerin-null myogenic progenitors to identify molecular pathways implicated in Emery-Dreifuss Muscular Dystrophy. Overall design: Total RNA was isolated from 2 million wildtype or emerin-null H2Ks during proliferation and at each day of differentiation using the miRNeasy Mini Kit (Qiagen, product #217004) and processed according to manufacturer's protocol. RNA was isolated from three independent cell culture plates for each sample.
Publication Title
Expression Profiling of Differentiating Emerin-Null Myogenic Progenitor Identifies Molecular Pathways Implicated in Their Impaired Differentiation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Rattus norvegicus
- 14 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Tenotomy is the release of muscle preload that causes abrupt shortening of the muscle and models atrophy and fibrosis without inflammatory response. Fibrosis in the skeletal muscle is known to be triggered by TGF-, which is activated by mediators of inflammatory events. As these were lacking, tenotomy provided an opportunity to investigate transcriptional events on a background without inflammation. An unbiased look at the transcriptome of tenotomy-immobilized soleus muscle revealed that the majority of the transcriptional changes took place in the first four weeks.
Publication Title
Tenotomy immobilization as a model to investigate skeletal muscle fibrosis (with emphasis on Secreted frizzled-related protein 2).
Sample Metadata Fields
Sex, Specimen part
View Samples- Bos taurus
- 6 Downloadable Samples
- Bovine Gene 1.0 ST Array (bovgene10st)
Description
In previous studies it has been shown that bovine granulosa cells (GC) cultured at a high plating density dramatically change their physiological and molecular characteristics, thus resembling an early stage of luteinization. During the present study, these specific effects on the GC transcriptome were comprehensively analysed of the same cell culture model comparing GC cultured at normal and high density.
Publication Title
Induction of altered gene expression profiles in cultured bovine granulosa cells at high cell density.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Developing osteoblasts undergo a sequence of three consecutive phases: cell proliferation, extracellular matrix maturation, and mineralization. We investigated pH effects on these phases using the osteoblast-like cell line MC3T3-E1.
Publication Title
MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST).
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
CD74, a Type II membrane glycoprotein and MHC class II chaperone (Ii), is normally expressed by cells associated with the immune system. CD74 also forms heterodimers with CD44 to generate receptors to macrophage migration inhibitory factor (MIF), a proinflammatory cytokine. Following targeted Cre-mediated deletion of Ikk in IkkDeltaHep mice (a strain highly susceptible to chemically-induced hepatotoxicity and hepatocarcinogenesis), CD74 is abundantly expressed by hepatocytes throughout liver acini (as detected by specific Western blots and immunohistochemical stains); it is not observed in either control IkkF/F hepatocytes or embryonic fibroblasts from Ikk-/- mice. Constitutive CD74 expression in IkkDeltaHep hepatocytes is also accompanied by significantly augmented expression of CD44 and genes associated with antigen processing and host defense. These observations suggest that IkkDeltaHep hepatocytes might directly respond to MIF signaling, accounting partly for the enhanced susceptibility of IkkDeltaHep mice to hepatotoxins and hepatocarcinogens, and also might exhibit unusual immunological properties including antigen presentation.
Publication Title
Targeted deletion of hepatocyte Ikkbeta confers growth advantages.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We used microarrays to globally profile the gene expression changes observed after 24h when transfecting antisense oligonucleotides in HuH77 cells
Publication Title
Managing the sequence-specificity of antisense oligonucleotides in drug discovery.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5’ and 3’ untranslated regions, typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons we unexpectedly show extremely common unbalanced expression of cognate 3’ UTR and CDS sequences, observing many genes with high UTR relative to CDS, and others with high CDS to UTR. By in situ hybridization 19 of 19 genes examined show a broad range of UTR to CDS expression ratios in different neurons and other tissues. These ratios may be spatially graded or change with developmental age, but are consistent across animals. Further, for two genes examined, a UTR to CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression. Our findings raise questions about the role of isolated UTR sequences in regulation of protein expression, and highlight the importance of separately examining UTR and CDS sequences in gene expression analyses. Overall design: dopamine or serotonin neuronal mRNA was purified selectively by using dopamine transporter (DAT) and SLC6A4 (serotonin transporter) BacTrap mice. RNA sequencing was carried out using Illumina HiSeq 2500.
Publication Title
Widespread Differential Expression of Coding Region and 3' UTR Sequences in Neurons and Other Tissues.
Sample Metadata Fields
Specimen part, Subject
View Samples