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Mus musculus
12 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Several transcription factors are known to be expressed in discrete regions of the otic vesicle and Dlx5 is one of those that is expressed highly in the presumptive dorsal vestibular region. Mice lacking Dlx5 have vestibular defects. Specifically, they fail to form the endolymphatic duct (a defect visible as early as E10) as well as the anterior and posterior semi-circular canals. The lateral canal does form but is smaller, whereas the saccule, the utricle and the cochlea appear relatively normal. The goal of this study was to use microarrays to identify differentially expressed genes between wild-type and Dlx5-null otic vesicles microdissected from E10 and 10.5 and identify downstream targets of Dlx5 by searching the immediate 3kb promoter regions of the differentially expressed genes for homeodomain binding sites followed by chromatin immunoprecipitation in an otic vesicle-derived cell line over-expressing Dlx5.
Publication Title
Identification of direct downstream targets of Dlx5 during early inner ear development.
Sample Metadata Fields
Age, Specimen part
View Samples
GSE4774- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Dlx homeobox genes have central roles in controlling patterning and differentiation of the brain and craniofacial primordia. In the brain, loss of Dlx function results in defects in the production, migration and differentiation of GABAergic neurons, that can lead to epilepsy. In the branchial arches, loss of Dlx function leads to craniofacial malformations that include trigeminal axon pathfinding defects. To determine how these genes function, we wish to identify the transcriptional circuitry that lies downstream of these transcription factors by comparing gene expression in wild type with Dlx mutant CNS and craniofacial tissues.
Publication Title
Dlx genes pattern mammalian jaw primordium by regulating both lower jaw-specific and upper jaw-specific genetic programs.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
Illumina HiSeq 2500
Description
Overview: We report here that gene expression in E13.5 wild type (WT) mouse lenses differs from the lenses of mice that conditionally lack the Prox1 transcription factor in the lens of their eyes (Prox1 cKO) as assayed by high throughput RNA sequencing (RNAseq). The methodology outlined herein is similar to a previous RNAseq experiment from our lab (Manthey et al., 2014a)(Geo ascension: GSE 49949), and the filtering and processing criteria for this experiment was published as well.(Manthey et al., 2014b). The mammalian lens is notable for its biased gene expression, where 90% of the observed protein is expressed by just 50 genes. RNAseq was employed to sequence past these highly expressed lens structural genes and report the relative abundance of both high and low expression genes. In this study we demonstrated that 642 genes were differentially expressed in the lenses of Prox1 cKOs as compared to WT lenses. These data were analyzed using the DAVID biostatical analysis package and we found that the expression of lens specific proteins, as well as cytoskeletal genes and genes that regulated the cytoskeleton were expressed at lower levels in Prox1 cKOs. This analysis showed that the expression of genes encoding extracellular matrix components and their regulators, as well as cell adhesion increased in Prox1 cKO lenses when compared to WTs. Description of Filtering Criteria: Our initial analysis identified 5,492 genes that were differentially expressed in Prox1 cKO lenses as compared to WTs as computed by Pair-wise qCML method exact tests with a Benjamini Hochberg false discovery rate correction greater than the threshold of P < 0.05. As we described previously, there is significant variation in gene expression between inbred C57Bl/6 <har> and mice with a mixed background below a threshold of 2.5 fold. For this reason we filtered out all genes whose differential expression was less than 2.5 fold. We also wanted to filter out genes that were expressed at such low levels that they were unlikely to impact cellular function. We restricted our list to those genes that were expressed at greater than 2 Reads per Kilobase per million reads (RPKM) in either WT or Prox1 cKO samples, a value which corresponds to approximately 1 mRNA molecule per cell. The application of these filtering criteria resulted in narrowing our list to 642 genes that were likely to impact the Prox1 cKO lens phenotype. Manthey, A. L., Lachke, S. A., FitzGerald, P. G., Mason, R. W., Scheiblin, D. A., McDonald, J. H. and Duncan, M. K. (2014a) ''Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development'', Mech Dev 131: 86-110. Manthey, A. L., Terrell, A. M., Lachke, S. A., Polson, S. W. and Duncan, M. K. (2014b) ''Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis'', Genom Data 2: 369-374. Overall design: RNA-Seq comparison of C57Bl/6 <har> wild type controls and Prox1 conditional knockout lenses at E13.5
Publication Title
Prox1 and fibroblast growth factor receptors form a novel regulatory loop controlling lens fiber differentiation and gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 225 Downloadable Samples
- Illumina HiSeq 2500
Description
Single-cell RNA-Seq RNA from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007389 Overall design: Single-cell RNA-Seq from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5.
Publication Title
Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 140 Downloadable Samples
- Illumina HiSeq 2500
Description
J14 ES cells differentiated into MGE-like cells. Three groups of single-cell preparations were analyzed: ES cells (undifferentiated), differentiated cells (unsorted, of which less than 10% are GFP+) and GFP+ differentiated cells. These are specified in the "group" sample characteristic, with values "ES", "Unsorted" and "GFP+" respectively. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007904 Overall design: J14 ES cells differentiated into MGE-like cells
Publication Title
Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
NK cells from NKDxIL15tg mice spleens and bone marrow were purified by FACS. NK cells from IL15tg mice spleens were purified by FACS.
Publication Title
Distal-less homeobox transcription factors regulate development and maturation of natural killer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Areas and layers of the cerebral cortex are specified by genetic programs that are initiated in progenitor cells and then, implemented in postmitotic neurons. Here, we report that Tbr1, a transcription factor expressed in postmitotic projection neurons, exerts positive and negative control over both regional (areal) and laminar identity. Tbr1 null mice exhibited profound defects of frontal cortex and layer 6 differentiation, as indicated by down-regulation of gene-expression markers such as Bcl6 and Cdh9. Conversely, genes that implement caudal cortex and layer 5 identity, such as Bhlhb5 and Fezf2, were up-regulated in Tbr1 mutants. Tbr1 implements frontal identity in part by direct promoter binding and activation of Auts2, a frontal cortex gene implicated in autism. Tbr1 regulates laminar identity in part by downstream activation or maintenance of Sox5, an important transcription factor controlling neuronal migration and corticofugal axon projections. Similar to Sox5 mutants, Tbr1 mutants exhibit ectopic axon projections to the hypothalamus and cerebral peduncle. Together, our findings show that Tbr1 coordinately regulates regional and laminar identity of postmitotic cortical neurons.
Publication Title
Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 15 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
We generated whole genome expression profiles from a homogeneous population of purified pacemaker neurons (ventral Lateral Neurons, LNvs) from wild type and clock mutant Drosophila. The study identifes a group of genes whose expression is highly enriched in LNvs compared to other neurons; and a second group of genes rhythmically expressed in LNvs in a clock-dependent manner.
Publication Title
A mechanism for circadian control of pacemaker neuron excitability.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 87 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Analysis of gene expression over serial 150um sections of a single gestational week 18 human neocortical specimen. The hypothesis tested with this dataset was that a transcriptional signature of GABAergic neurons could be isolated via unsupervised gene coexpression analysis due to variation in the abundance of this cell type from section to section. This dataset is the second of its kind generated using this method (Gene Coexpression Analysis of Serial Sections, or GCASS).
Publication Title
Secretagogin is Expressed by Developing Neocortical GABAergic Neurons in Humans but not Mice and Increases Neurite Arbor Size and Complexity.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 21 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
To characterize the molecular origin of primary lymphomas of the central nervous system (PCNSL), 21 PCNSL of immunocompetent patients were investigated by microarray-based gene expression profiling. Comparison of the transcriptional profile of PCNSL with various normal and neoplastic B cell subsets demonstrated PCNSL (i) to display gene expression patterns most closely related to late germinal center B cells, (ii) to display a gene expression profile similar to systemic diffuse large B cell lymphomas (DLBCL), and (iii) to be in part assigned to the activated B cell-like (ABC) or the germinal center B cell-like (GCB) subtype of DLBCL.
Publication Title
Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell.
Sample Metadata Fields
No sample metadata fields
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