Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA227332 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Enhancer landscape of mouse developing midbrain at 11.5 dpc embryos
| PRJNA214614 | ENA
Project description:We report the distribution of interactive sites with the sequence close from Meis2 promoter within the genome of mouse embryonic forebrain. We prepared the chromatin from 11 dpc embryonic forebrain and made 3C (chromosomal conformation capture) library. High-throughput sequencing applied for the 3C analysis revealed the distribution of modified interactive sites within developing forebrain. 4C-seq analysis of mouse 11 dpc embryonic forebrain with the sequence close from Meis2 promoter. Forebrain isolated and disected from 11 dpc embryos are fixed by 1% formaldehyde. After conventional 3C reaction, 3C library for highthroughput sequence is prepared by combination of adaptor ligation and nesting PCR reactions.
2014-01-15 | E-GEOD-52281 | biostudies-arrayexpress
Project description:We report the distribution of histone H3K4me1 and H3K27ac within the genome of mouse embryonic forebrain. We prepared the chromatin from 11 dpc embryonic forebrain and made chromatin precipitation with antibody against H3K4me1 and H3K27ac (rabbit polyclonal antibody). High-throughput sequencing applied for the ChIP analysis revealed the differential distribution of modified histone within developing forebrain.
2014-11-12 | GSE52280 | GEO
Project description:The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. While many of the genes required for its development have been identified, the distant‐acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified over 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web‐based enhancer atlas comprising over 33,000 sections. We show how this large collection of annotated telencephalon enhancers can be used to study the regulatory architecture of individual genes, to examine the sequence motif content of enhancers, and to drive targeted reporter or effector protein expression in experimental applications. Furthermore, we used epigenomic analysis of human and mouse cortex tissue to directly compare the genome‐wide enhancer architecture in these species. This atlas provides a primary resource for investigating gene regulatory mechanisms of telencephalon development and enables studies of the role of distant‐acting enhancers in neurodevelopmental disorders. Examination of p300 binding in mouse embryonic stage 11.5 forebrain, mouse postnatal (P0) cortex tissue and human fetal (gestational week 20) cortex
2013-01-29 | E-GEOD-42881 | biostudies-arrayexpress
Project description:We report the distribution of interactive sites with the sequence close from Meis2 promoter within the genome of mouse embryonic forebrain. We prepared the chromatin from 11 dpc embryonic forebrain and made 3C (chromosomal conformation capture) library. High-throughput sequencing applied for the 3C analysis revealed the distribution of modified interactive sites within developing forebrain.
2014-01-15 | GSE52281 | GEO
Project description:We report the distribution of RING1B (one of Polycomb group factors) within the genome of mouse embryonic tissues. We prepared the chromatin from 11 dpc embryonic forebrain, midbrain, and forelimb buds and made chromatin precipitation with antibody against RING1B (mouse monoclonal antibody). High-throughput sequencing applied for the ChIP analysis revealed the differential distribution of RING1B protein among embryonic tissues. ChIP analysis of mouse 11 dpc embryonic forebrain, midbrain and forelimb buds against anti-RING1B antibody.
2014-01-14 | E-GEOD-48464 | biostudies-arrayexpress
Project description:Lmx1b regulates dorsalization of limb fates, but the mechanism of this regulation has not been characterized. To identify candidate genes regulated by Lmx1b we compared the limbs from Lmx1b KO mice to wild type mice during limb dorsalization (e11.5-13.5). Differentially expressed genes that we common to all three stages examined were considered to be likely candidates for Lmx1b regulation and further evaluated. At 11.5 and 12.5 dpc, embryos were harvested and the limb buds with the limb girdles were isolated. Embryos at 13.5dpc were also harvested and their distal limb buds (zeugopods and autopods) were isolated. Embryos were genotyped to confirm Lmx1b homozygosity (-/- or +/+). RNA from embryonic forelimbs and hindlimbs of wild type (WT) and Lmx1b KO mice was harvested using the Rneasy Kit (Qiagen). RNA was pooled to decrease genetic variability, i.e., six limbs at 11.5 dpc, three limbs at 12.5 dpc and six limbs at 13.5 dpc. Duplicate samples were generated using different embryos for each stage and then hybridized to the Affymetrix GeneChip® Mouse Genome 430 2.0 Array (UCI, Irvine, CA).
2012-05-21 | E-GEOD-34732 | biostudies-arrayexpress
Project description:The aim of this study was to analyze the gene expression profile for three main cell lines (supporting, interstitial/stromal, and germ cells) isolated from developing gonads at the critical period of sexual differentiation (between 11.5, and 13.5 dpc). Three cell lines (supporting, interstitial/stromal, and germ cells) were isolated from murine fetal XX and XY gonads at three time points (11.5, 12.5, and 13.5 dpc). Transgenic mouse strains with the expression of cell type specific fluorescent markers were used to isolate the cell lines. Cells were sorted using FACS method and then the RNA was extracted.
2016-08-09 | E-GEOD-85267 | biostudies-arrayexpress
Project description:Mus musculus Transcriptome at 3 developmental stages (11.5 dpc, 12.5 dpc, 13.5 dpc).
| PRJNA674495 | ENA
Project description:Understanding congenital liver disease requires elucidation of the signaling pathways and transcriptional events in the developing liver. Comprehensive assessment of gene expression between 10.5 and 16.5 dpc in the developing mouse liver and comparison with adult liver and non-hepatic embryonic tissue was validated with real-time PCR and in situ hybridization. The broad nature of the analysis provides insights into patterns of genetic control of hepatogenesis. Pathways implicated in human disease are highly regulated at the transcriptional level. Rather than activating or inhibiting a pathway or biological process by altering the expression of a single signaling molecule, transcriptional changes in large numbers of genes in a pathway or process are regulated in a coordinated manner. For example, both TGF-beta and Notch signaling is inhibited during hepatogenesis not just by decreasing transcription of multiple pathway members, but also with a complementary increase in the transcription of a pathway inhibitor. Similarly, genes related to specific biological processes exhibit strong temporal synchronization in which multiple members of the pathway have similar transcriptional regulation over time. Global coordination of signaling or functional families at the transcriptional level may be a mechanism to produce robustness of the desired outcomes. In addition, this comprehensive analysis provides a database for the further study of transcriptional events during liver development by identifying liver-specific, highly regulated genes. Experiment Overall Design: In order to provide transcriptional profile of the developing liver compared both to normal adult liver and non-hepatic embryonic tissueswe performed high-density microarray analysis using Affymetrix MG 430 2.0 chips for embryonic liver samples at 10.5, 11.5, 12.5, 13.5, 14.5, and 16.5 days post conception (dpc), embryo-minus liver tissues at 10.5, 11.5, 12.5, and 14.5 dpc, and normal 10-week-old adult mouse liver. Each sample consisted of at least five embryos.
2008-06-11 | E-GEOD-11201 | biostudies-arrayexpress