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Mus musculus
10 Downloadable Samples
Illumina Genome Analyzer II
Description
To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (CGNs) grown on an axonal growth permissive substrate. The goal of the analysis was to uncover neuronal type specific isoforms as a prelude to understanding patterns of gene expression underlying their intrinsic growth abilities. Global gene expression patterns were comparable to those found for other cell types, in that a vast majority of genes were expressed at low abundance. Nearly 18% of gene loci produced more than one transcript. More than 8000 isoforms were differentially expressed, either to different degrees in different neuronal types or uniquely expressed in one or the other. Sensory neurons expressed a larger number of genes and gene isoforms than did CGNs. To begin to understand the mechanisms responsible for the differential gene/isoform expression we identified transcription factor binding sites present specifically in the upstream genomic sequences of differentially expressed isoforms, and analyzed the 3’ untranslated regions (3’ UTRs) for microRNA (miRNA) target sites. Our analysis defines isoform diversity for two neuronal types with diverse axon growth capabilities and begins to illuminate the complex transcriptional landscape in two neuronal populations. Overall design: RNA was sequenced from cultured peripheral neurons of the dorsal root ganglia (DRG neurons) and cerebellar granular neurons (CGNs) of the central nervous system
Publication Title
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq.
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Sample Metadata Fields
Specimen part, Cell line, Subject
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SRP044619- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2000
Description
To identify isoform differential expression underlying peripheral nerve regeneration we performed RNA-Sequencing on DRG neurons after axotomy. Overall design: RNA was sequenced from peripheral Dorsal Root Ganglia (DRG) neurons from adult male mice 7 days after a conditioning lesion at the level of the sciatic nerve (Crushed samples) or after a sham surgery (Controls surgery).
Publication Title
Identification of miRNAs involved in DRG neurite outgrowth and their putative targets.
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Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Cerebellum from post-natal day 11 L1 knockout mice on the 129Sv background were compared to wild type littermates. The original goal of the study was to determine if there was compensation from other L1 family members or alterations in cell survival or apoptosis. Interestingly no major changes were detected in those families or pathways.
Publication Title
A modifier locus on chromosome 5 contributes to L1 cell adhesion molecule X-linked hydrocephalus in mice.
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Sex
View Samples- Rattus norvegicus
- 4 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Unlike other terminally differentiated cell types, vascular SMCs display remarkable phenotypic plasticity. The adult, differentiated state is traditionally defined by expression of well-characterized SMC contractile genes. Extracellular cues, however, can induce contractile SMCs to remodel toward a synthetic state characterized by a spectrum of proliferative, migratory, and inflammatory phenotypes.
Publication Title
Integrative genomics identifies DSCR1 (RCAN1) as a novel NFAT-dependent mediator of phenotypic modulation in vascular smooth muscle cells.
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Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: The goals of this study are to identify the transcriptional profile of retinal ganglion cells (RGCs) with the capacity to regenerate an axon, and contrast this profile with the profile of RGCs that cannot regenerate an axon. Methods: See sample pages for protocols for tissue preparation, RNA extraction and purification, library construction and data processing. Results: RNA from the 12 samples was sequenced to an average depth of 42 million reads. Genes were considered expressed if a gene had an expression of 1 count per million in 3 of the 12 samples. There were 13,406 genes that met this criterion. Conclusions: Our study represents the first analysis by NGS of highly-purified RGCs in the context of axonal injury Overall design: RGC mRNA profiles of melanopsin RGCs and ON-OFF Direction Selective Ganglion Cells (ooDSGCs) were generated by deep sequencing in triplicate, using Illumina HiSeq 2500.
Publication Title
Thrombospondin-1 Mediates Axon Regeneration in Retinal Ganglion Cells.
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Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix HT Human Genome U133A Array (hthgu133a)
Description
Although an important association between lymph node metastasis and poor prognosis in breast cancer was observed decades ago, an active role for the lymphatic system in metastatic dissemination has only recently been examined. We demonstrate that the Six1 homeoprotein promotes peri- and intra-tumoral lymphangiogenesis, lymphatic invasion, and distant metastasis of breast cancer cells. We identify the pro-lymphangiogenic factor, VEGF-C, as required for this process, and demonstrate transcriptional induction as the mechanism of regulation of VEGF-C expression by Six1. Using a different, but complementary animal model, we show that while required, VEGF-C is not sufficient for the pro-metastatic effects of Six1. Verifying the clinical significance of this pro-metastatic Six1-VEGF-C axis, we demonstrate co-expression of Six1 and VEGF-C in human breast cancer.
Publication Title
SIX1 induces lymphangiogenesis and metastasis via upregulation of VEGF-C in mouse models of breast cancer.
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Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 175 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Microarrays were used to investigate the the effect of vedolizumab (VDZ) therapy on colonic mucosal gene expression in UC patients and compared the changes to those observed with infliximab (IFX) therapy.
Publication Title
Effect of vedolizumab (anti-α4β7-integrin) therapy on histological healing and mucosal gene expression in patients with UC.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Growth factor independence 1b (gfi1b) is important for the maturation of erythroid cells and the regulation of embryonic globin expression.
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Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Growth factor independence 1b (Gfi1b) is a DNA binding repressor of transcription with vital functions in hematopoiesis. Gfi1b-null embryos die at midgestation very likely due to defects in erythro- and megakaryopoiesis. To analyze the full functionality of Gfi1b in embryonic erythropoiesis, we used conditionally deficient mice that harbor floxed Gfi1b alleles and one EpoR-Cre knock-in allele.
Publication Title
Growth factor independence 1b (gfi1b) is important for the maturation of erythroid cells and the regulation of embryonic globin expression.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Growth factor independence 1b (Gfi1b) is a DNA binding repressor of transcription with vital functions in hematopoiesis. Gfi1b-null embryos die at midgestation very likely due to defects in erythro- and megakaryopoiesis. To analyze the full functionality of Gfi1b in erythropoiesis, we used conditionally deficient mice that harbor floxed Gfi1b alleles and the Mx-Cre transgene inducible by pIpC treatment.
Publication Title
Growth factor independence 1b (gfi1b) is important for the maturation of erythroid cells and the regulation of embryonic globin expression.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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