RNAseq analysis comparing siRNA knocked down FOXF2 in and MKX in human normotrophic scar dermal fibroblasts
Ontology highlight
ABSTRACT: 3mm punch biopsies were taken from a healed normotrophic scar in burn patients with a scar at least 1 year old and fibroblasts were cultured from explants. Previous transcriptomic and epigenomic work found MKX and FOXF2 genes were overexpressed and these were knocked down using siRNA. RNA was then extracted and analysed using RNAseq to determine genes and pathways affected by this knockdown
Project description:3mm punch biopsies were taken from a healed normotrophic scar and a contralateral matched control site in burn patients with a scar at least 1 year old. Fibroblasts were cultured from explants to passage 2 and RNA was extracted and run on expression arrays to examine differences in scar and control fibroblast gene expression Normotrophic scar maintains its abnormal scar phenotype for the rest of the patients life, long after the injury has healed. Differences in gene expression may reaveal target genes that can be modulated to improve scar appearance
Project description:3mm punch biopsies were taken from a healed normotrophic scar and a contralateral matched control site in burn patients with a scar at least 1 year old. Fibroblasts were cultured from explants to passage 2 and DNA was extracted and run on methylation arrays to examine differences in scar and control fibroblast gene expression Normotrophic scar maintains its abnormal scar phenotype for the rest of the patients life, long after the injury has healed. Differences in gene expression may reaveal target genes that can be modulated to improve scar appearance
Project description:Tendons are crucial connective tissues that link muscle to bone. We have demonstrated that the transcription factor Mkx plays a pivotal role in tendon development and homeostasis by regulating collagen fibril organization through tendon cell fate determination from progenitor cells and promoting the expression of type I collagen and proteoglycans. However, the precise role of Mkx in tendon homeostasis after birth is not well understood. Therefore, we generated conditional Mkx knockout mice by crossing Mkx-CreER mice with Mkx floxed mice. Following tamoxifen administration, we performed transcriptome analysis of tendons from control mice (Mkx-CreER/+ and Mkx flox/+) and Mkx conditional knockout mice (Mkx-CreER/flox)
Project description:Analysis of C3H10T1/2 cells overexpressing Mkx. This microarray results show that Mkx has the potential ability to promote differentiation to tendon, ligament and annulus fibrosus cells.
Project description:To identify the genes and pathways regulated by FOXF2, we investigated potential FOXF2 gene targets by microarray analyses of primary prostate stromal cells (PrSC) in which FOXF2 was knocked down by siRNA. 190 differentially expressed genes were selected, of which 104 genes were more highly expressed in PrSC cells treated with FOXF2 siRNA and 86 were more highly expressed in PRSC cells treated with negative control siRNA. Experiment Overall Design: In each experiment, we compared gene expression of PrSC cells treated with FOXF2 siRNA versus PrSC cells treated with negative control siRNA, in a total of 6 affymetrix arrays. 190 differentially expressed genes were selected (ratio negative control siRNA/siRNA ⥠2log |0.8| as average in all arrays).
Project description:Brain of the foxf2 mutant mouse embryo shows microvascular aneurysm, underdeveloped blood brain barrier and also significant defects in the tissue integrity. Foxf2 expresses in the pericytes of the brain and seem to play an important role in proper development of the BBB. Brains of E18.5 wt and foxf2 mutant mouse embryos dissected and RNA extracted from the brains using Sigma mammalian total RNA extraction kit. The RNA then been sent to th core facility for hybridization.
Project description:To identify the genes and pathways regulated by FOXF2, we investigated potential FOXF2 gene targets by microarray analyses of primary prostate stromal cells (PrSC) in which FOXF2 was knocked down by siRNA. 190 differentially expressed genes were selected, of which 104 genes were more highly expressed in PrSC cells treated with FOXF2 siRNA and 86 were more highly expressed in PRSC cells treated with negative control siRNA.