ATAC-seq, histone-seq, and RNA-seq of mouse craniofacial tissues [RNA-seq]
Ontology highlight
ABSTRACT: To investigate the role of the transcription factor AP-2 in craniofacial development, we performed: ATAC-seq on E11.5 craniofacial surface ectoderm in control and Tfap2a/Tfap2b ectoderm knock-out embryos; RNA-seq on E10.5 craniofacial prominences from control and Tfap2a/Tfap2b ectoderm knock-out embryos; histone-seq (H3K4me3) in E10.5 and E11.5 wild-type craniofacial surface ectoderm.
Project description:To investigate the role of the transcription factor AP-2 in craniofacial development, we performed: ATAC-seq on E11.5 craniofacial surface ectoderm in control and Tfap2a/Tfap2b ectoderm knock-out embryos; RNA-seq on E10.5 craniofacial prominences from control and Tfap2a/Tfap2b ectoderm knock-out embryos; histone-seq (H3K4me3) in E10.5 and E11.5 wild-type craniofacial surface ectoderm.
Project description:To investigate the role of the transcription factor AP-2 in craniofacial development, we performed: ATAC-seq on E11.5 craniofacial surface ectoderm in control and Tfap2a/Tfap2b ectoderm knock-out embryos; RNA-seq on E10.5 craniofacial prominences from control and Tfap2a/Tfap2b ectoderm knock-out embryos; histone-seq (H3K4me3) in E10.5 and E11.5 wild-type craniofacial surface ectoderm.
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.
Project description:Wild type or CBP/p300 fx/fx; Pax6-Cre-positive (CBP/p300-/-) surface ectoderm from E10.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified, pooled for each genotype and triplicate samples were reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6v2.0 bead arrays.
Project description:This investigation provides a robust multi-dimensional compendium of gene expression data relevant to mouse facial development. It profiles the transcriptome ofectoderm and mesenchyme from the three facial prominences in a time series encompassing their growth and fusion. Analysis of the dataset identified more than 8000 differentially expressed genes comprising dramatically different ectoderm and mesenchyme programs. The mesenchyme programs included many genes identified in earlier analyses as well hundreds of genes not previously implicated in craniofacial development. The ectoderm programs included over a thousand genes that highlight epithelial structure, cell-cell interactions and signaling. The dataset includes 45 .cel files, DABG probability and RMA log2 expression values for each probeset, and statistics for 9457 probesets representing 8575 genes. 45 total samples, with 15 conditions sampling three ages (E10.5, E11.5, E12.5), three facial prominences (mandibular, maxillary and fronto-nasal) and two tissue layers (ectoderm or mesenchyme), with 3 biological replicates per condition. Differential expression was determined after median filter for variance with three-way ANOVA, Benjamini-Hochberg multiple testing correction
Project description:Neo/null loss of Tfap2a in E10.5 mouse facial prominences triplicate run comparing tissue dissected from the nasal, maxillary and mandibular comparing AP-2 mutant and control embryos
Project description:We report gene expression patterns in embryonic mice (E8.5, E9.5, E10.5) through RNA-seq of 13 tissue/stage combinations in order to generage an atlas of early mouse craniofacial gene expression. Embryos at E8.5, E9.5, and E10.5 CD1 were collected from CD1 mice, fom multiple micro-regions whose development, differentiation and signaling are responsible for the construction of the mammalian face.
Project description:Wild type or CBP/p300 fx/fx; Pax6-Cre-positive (CBP/p300-/-) surface ectoderm from E10.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified, pooled for each genotype and triplicate samples were reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6v2.0 bead arrays. Three wild type and three knockout embryos were used. The RNA from embryos of the same genotype was purified and pooled and triplicate samples were amplified and used for microarray analysis.