E-MTAB-5671
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-5671 | ExpressionAtlas | 2019-05-14
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-5671-analysis-methods.tsv | Tabular | |||
| E-MTAB-5671-analytics.tsv | Tabular | |||
| E-MTAB-5671-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-5671-configuration.xml | Xml | |||
| E-MTAB-5671-g2_g3-mvaPlot.png | Other |
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Project description:RNA-seq of E10.5 limb mesenchymal cells from mice with mutations in Mycn and mir17-92
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Project description:Numerous studies have established a critical role for BMP signaling in skeletal development. In the developing axial skeleton, sequential SHH and BMP signals are required for specification of a chondrogenic fate in somitic tissue. A similar paradigm is thought to operate in the limb, but the signals involved are unclear. To investigate the nature of these signals we examined BMP action in mesenchymal populations derived from the early murine limb bud (~ E10.5). These populations exhibited a graded response to BMPs, in which early limb mesenchymal (EL) cells (from the distal hind limb) displayed an anti-chondrogenic response, whereas BMPs promoted chondrogenesis in older cell populations. To better understand the molecular basis of disparate BMP action in these various populations, gene expression profiling with Affymetrix microarrays was employed to identify BMP-regulated genes. These analyses showed that BMPs induced a distinct gene expression pattern in the EL cultures versus later mesenchymal limb populations (IM and LT). Mouse embryos at gestational age E10.5 were collected and various portions of the limb were micro-dissected. These led to the generation of three populations of cells, early (EL) limb mesenchymal cells from the distal half of the hind limb, an intermediate (IM) population derived from the distal 1/3 of the fore limb, and a later (LT) population from the proximal 2/3 of the fore limb. Mesenchymal cells were isolated and cultured with and without BMP4 treatment. RNA was extracted from cultures at either Day 0,1 or 2, labelled and hybridized to Affymetrix 430 2.0 microarrays. For each time point, RNA was collected from two biological replicates for each treatment condition.
2010-04-12 | E-GEOD-20398 | biostudies-arrayexpress
Project description:Mice with conditionally deactivating mutations in Mycn (Mycnfl/fl) or mir17-92 & mir106b (mir17-92fl/fl ; mir106b-/-) were crossed with mice expressing Cre-recombinase driven by the Prx1 promoter (Prx1Cre). Embryos were collected at E10.5, and distal compartment of hind- and fore-limbs were isolated from wild-type and conditional knock-out embryos (n=3 replicates per biologic group). Total RNA was extracted from each specimen with Trizol, and used in RNA-seq library preparation with Illumina Truseq mRNA library kit. Libraries were sequenced on the Illumina NextSeq system with 75bp single end reads.
2017-05-24 | E-MTAB-5671 | biostudies-arrayexpress
Project description:Mutations in the transcription factor p63 underlie of a series of human malformation syndromes which are defined by a combination of epidermal, limb and craniofacial abnormalities including cleft lip and palate. Transcription profiling was performed to determine the role of p63 in vivo mouse palatal shelves. RNA-seq analysis was done of palatal shelves dissected from E10.5, E11.5, E12.5, E13.5 and E14.5 mouse embryos.
2017-06-12 | E-MTAB-3157 | biostudies-arrayexpress
Project description:The basic helix-loop-helix transcription factor Twist1 has a well-documented role in mesenchymal populations of the developing embryo, such as endocardial cushion (ECC) mesenchymal cells and limb buds, and during cancer development and progression. Whether Twist1 regulates the same transcriptional targets in different cell types has yet to be investigated. Through chromatin immunoprecipitation followed by sequencing (Chip-seq) analysis, the cell type-specific genome-wide occupancy of Twist1 was investigated in ECCs, limb buds and mouse peripheral nerve sheath tumor (PNST) cells. Twist1 binds mainly in a cell type-specific manner, with very few common genomic regions occupied by Twist1 in different cell types. Genes associated with binding peaks in each cell type are related to known Twist1 cellular functions in ECCs, limb buds, and cancer cells. We found that cell type-specific binding of Twist1 may be influenced by histone modifications or co-factors. Binding regions were located in several Wnt pathway associated genes, supporting a link between Twist1 and Wnt signalling in ECCs, limb buds, and PNST cells. These data suggest that similar functions are regulated by Twist1 in ECCs, limb buds, and PNST cells in a cell type-specific manner, and provide insights into possible mechanisms utilized for cell type-specificity of Twist1 binding. We compare Twist1 genome occupancy in mouse embryonic day (E) 12.5 endocardial cushion mesenchymal cells, E10.5 forelimb buds, and a mouse peripheral nerve sheath tumor cell line.
2014-10-02 | E-GEOD-50111 | biostudies-arrayexpress
Project description:Comparing gene expression of cells from the E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS. Keywords: comparison, cell-type comparison, experiemental versus control
2008-01-01 | GSE7598 | GEO
Project description:The mechanism driving the remarkable ability of the remaining kidney to enlarge and increase its function following the removal of its contralateral pair remains elusive. To explore the pathways driving compensatory renal hypertrophy, comprehensive RNA-seq transcriptional studies were undertaken in the kidneys of C57BL/6 mice undergoing hypertrophy at 24, 48, and 72 hours following nephrectomy, and these results were compared with mice undergoing sham operations. In addition, mass spectrometry was carried out at 24 hours to examine changes in protein expression. Single-nuclei RNA-Seq was used to delineate bulk RNA-seq data into cell types at 24 hours post-nephrectomy. HK-2 renal tubular cells were examined for their ability to undergo hypertrophy in the presence of IGF-1 via the activation of cholesterol biosynthesis pathways. Bulk RNA-seq revealed substantial time-dependent enhancement of cholesterol biosynthesis pathways, increases in mitochondrial gene expression, and cell cycle perturbations. Single-nuclei RNA-Seq at 24 hours post-nephrectomy showed that Sterol Binding Protein 2 (SREBP2) activity increases in medullary thick ascending limb cells and, to a lesser extent, in proximal tubular cells, consistent with the role of promoting cholesterol synthesis. Furthermore, SREBP2 was found to regulate cell size following IGF-1 stimulation in HK-2 cells. There are early, cell-specific alterations in gene expression of cholesterol biosynthesis pathways, mitochondrial genes, and the cell cycle in kidneys undergoing compensatory hypertrophy. SREBP2 activity in the medullary thick ascending limb and, to a lesser extent, in proximal tubules may play a previously undescribed role in promoting cholesterol metabolism in the mechanism underlying compensatory renal hypertrophy.
2024-07-19 | PXD047516 | Pride
Project description:Comparing gene expression of cells from the E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS. Experiment Overall Design: 8 samples, 4 ZPA and 4 rest of the limb
2008-06-15 | E-GEOD-7598 | biostudies-arrayexpress
Project description:The transcriptomes of immortalized anterior and posterior limb cell lines derived from E10.5 embryos were compared. Total RNA extracted from three E10.5 anterior and posterior limb cell line samples were compared.
2012-09-18 | E-GEOD-38370 | biostudies-arrayexpress
Project description:Numerous studies have established a critical role for BMP signaling in skeletal development. In the developing axial skeleton, sequential SHH and BMP signals are required for specification of a chondrogenic fate in somitic tissue. A similar paradigm is thought to operate in the limb, but the signals involved are unclear. To investigate the nature of these signals we examined BMP action in mesenchymal populations derived from the early murine limb bud (~ E10.5). These populations exhibited a graded response to BMPs, in which early limb mesenchymal (EL) cells (from the distal hind limb) displayed an anti-chondrogenic response, whereas BMPs promoted chondrogenesis in older cell populations. To better understand the molecular basis of disparate BMP action in these various populations, gene expression profiling with Affymetrix microarrays was employed to identify BMP-regulated genes. These analyses showed that BMPs induced a distinct gene expression pattern in the EL cultures versus later mesenchymal limb populations (IM and LT).
2010-04-01 | GSE20398 | GEO