MeDIP-on-Chip for the Ciliary derived stem/progenitor cells and their differentiated progeny.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Genotypic technology
PROVIDER: E-GEOD-64546 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Whole genome profiling of histone methylation (H3K4me3, H3K27me3 and RNA Pol II) in Ciliary derived stem/progenitor cells and differentiated cells. In the present study we focus on the cellular differentiation that involves loss of pluripotency and gain of lineage and cell type-specific characteristics and we show developments from adult ciliary derived stem/progenitor cells to differentiated retinal neurons/glial cells of human cadaveric eyes in vitro. Ciliary pigment epithelial cells isolated from human cadaveric eye balls were cultured in the presence of mitogens like Epidermal Growth Factor (EGF) and Fibroblast Growth Factors (FGF) to generate neurospheres (Stem/progenitor population). The generated neurospheres were plated on laminin and poly-D-lysine-coated cover slips in the presence of the Brain derived neurotrophic factor (BDNF), Retinoic acid (RA) and 10% FBS for the differentiation (Retinal neuron/glial cells). Global Methylation patterns of histone H3K4me3, RNA Pol II and H3K27me3 were analysed in the present study. This work would provide an outline of epigenetic modifications in ciliary derived stem/progenitor cells and the progeny that underwent differentiation into retinal neurons/glial cells and present that specific histone methylations are involved in gene expression reprogramming during the process of differentiation.
2016-07-04 | E-GEOD-65268 | biostudies-arrayexpress
Project description:To find novel targets regulated by AR upon DHT stimaulation at 24 hours of time point Agilent two-color ChIP on chip experiment, Organism: Homo sapiens , Agilent 2X400K Human Promoter array (AMADID: G4874A_27954)
2016-09-02 | E-GEOD-72438 | biostudies-arrayexpress
Project description:Salivarian trypanosomes cause human sleeping sickness and economically important livestock diseases, transmitted by Tsetse flies and replicating extracellularly throughout the life cycle. The surface of "bloodstream forms", which live within mammals, is coated by a monolayer of a Variant Surface Glycoprotein (VSG). Switching of the expressed VSG gene enables the parasites to evade adaptive immunity. Up until now, the mechanism by which VSG mRNA stability is maintained was unknown. To identify proteins specifically interacting with VSG mRNA (and alpha tubulin as control), we performed RNA-antisense purifications (RAP) following instructions published by McHugh et al. 2018 with some modifications.
2021-04-14 | PXD021772 | Pride
Project description:Claudin (CLDN) proteins are commonly expressed in cancers and accordingly targeted in novel therapeutic approaches. C-terminus of Clostridium perfringens enterotoxin (C-CPE) binds efficiently several claudins and can be used to specifically target cancer cells. This experiment used RNA-seq to profile gene expression changes of native and FusionRed transfected canine tumor cell lines;TihoDTCC0840 (0840) and TihoDProAdCarc0846 (0846) after a 3 hours of C-CPE treatment (20µg/ml).
2021-11-30 | E-MTAB-10839 | biostudies-arrayexpress
Project description:Enterotoxin-producing C. perfringens type A is a common cause of food poisonings. The cpe encoding the enterotoxin can be chromosomal (genotype IS1470) or plasmid-borne (genotypes IS1470-like-cpe or IS1151-cpe). The chromosomal cpe-carrying C. perfringens are a more common cause of food poisonings than plasmid-borne cpe-genotypes. The chromosomal cpe-carrying C. perfringens type A strains are generally more resistant to most food-processing conditions than plasmid-borne cpe-carrying strains. On the other hand, the plasmid-borne cpe-positive genotypes are more commonly found in human feces than chromosomal cpe-positive genotypes, and humans seem to be a reservoir for plasmid-borne cpe-carrying strains. Thus, it is possible that the epidemiology of C. perfringes type A food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains is different. A DNA microarray was designed for analysis of genetic relatedness between the different cpe-positive and cpe-negative genotypes of C. perfringens strains isolated from human, animal, environmental and food samples. The DNA microarray contained two probes for all protein-coding sequences in the three genome-sequenced strains (C. perfringens type A strains 13, ATCC13124, and SM101). The chromosomal and plasmid-borne C. perfringens genotypes were grouped into two distinct clusters, one consisting of the chromosomal cpe-genotypes and the other consisting of plasmid-borne cpe-genotypes. Analysis of the variable gene pool complemented with the growth studies demonstrate different carbohydrate and amine metabolism in the chromosomal and plasmid-borne cpe-carrying strains, suggesting different epidemiology of the cpe-positive C. perfringens strain groups. Array CGH. Two-color hybridizations on 8x15K Agilent arrays. Eight reference strain hybridizations. Normalization was based on log-ratios against the reference strain. For each sample, 8 normalization factors were calculated, one against each reference hybridization, and the median normalization factor was used. This was repeated for each sample hybridization separately.
2012-03-01 | E-GEOD-30954 | biostudies-arrayexpress
Project description:DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-controlled DMRs provided an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at the cis-controlled DMRs during NIL population development. DNA methylation level was associated with local genotypes in all of the >30,000 examined cases except one. Additionally, the majority of the DMRs were not associated with small RNA. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits cis-controlled inheritance patterns, is highly stable and does not require active programming by small RNAs for maintenance. Methylation profiles in seedling tissue of maize near-isogenic lines (NILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array.
2014-04-01 | E-GEOD-51567 | biostudies-arrayexpress
Project description:Plant-derived secondary metabolites found in animal feed sources are beneficial for nutrition and health. Cowpea is a protein and phenolic-rich forage used as feed resource in animal system. The objective of this study was to understand the effect of cowpea secondary metabolites on gene expression in cows blood in vitro. Whole blood collected from Holstein Friesian cows (n=5) were treated with 10 ug/ml of cowpea leaf phenolic extract and untreated samples served as control. Total RNA was isolated and pooled together for microarray analysis. The Agilent one color bovine (v2) 4x44KÂ array was used and preliminary gene expression profiles generated using Cy3 labeled cDNA from CPE-stimulated and untreated samples. Gene expression analysis revealed a total of 3170 differentially expressed genes- 1716 up regulated and 1454 down regulated genes respectively. Pathway analysis identified CPE treatment association with innate immune response pathways including Toll-like receptor (TLR) signaling pathway, the Wnt signaling pathway, inflammation response pathway, and increased expression of the transcription factor NFKB1 were observed. Treatment with CPE decreased the expression of proinflammatory cytokines IL1A, IL1B and IL21. Quantitative real time PCR was performed to validate some gene members of the Toll-like receptor, inflammation response and Wnt signaling pathways. In vitro treatment with CPE impacted global gene expression profile in cow blood and results obtained in this study shows the potential immuno-modulatory properties of cowpea feed phenolic in cows. The global gene expression of the effect of cowpea phenolic extract (CPE) was measured in bovine peripheral blood.The experiment involved two groups; cowpea phenolic extract (CPE) treated samples vs untreated control group. Pooled RNA samples from each group was hybridized on Agilent one color bovine (v2) 4x44KÂ microarray slides. Two slides were prepared each with 4 array compartment.
2015-11-21 | E-GEOD-75239 | biostudies-arrayexpress
Project description:Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize. meDIP-chip analysis of four maize tissues identifed few tissue-specific DNA methylation variable regions (tDMRs), whereas hundreds of genotype-specific DMRs were identified that were conserved across tissues. Methylation profiles for tassel, embryo, endosperm, and leaf of the maize inbred lines B73 and Mo17. Three biological replications for each tissue of each genotype were performed. A custom 2.1M NimbleGen array (GPL13499) was used for embryo, endosperm, and leaf, and a custom 3x1.4M NimbleGen array containing a subset of probes from the 2.1M NimbleGen array (GPL15621) was used for tassel. All of the processed data is based on the largest number of comparable probes (~1.4M) between the two arrays.
2012-08-27 | E-GEOD-38503 | biostudies-arrayexpress
Project description:DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, other genetic changes such as transposon insertions also can lead to changes in DNA methylation levels. Genome-wide profiles of DNA methylation levels for 20 maize inbreds were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize genotypes resulting in the discovery of 1,966 common DMRs and 1,754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with SNPs found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the DNA methylation variation. The analysis of gene expression in the same samples used for DNA methylation profiling identifies over 300 genes with expression patterns that are significantly associated with the DNA methylation variation among genotypes. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic variation is often stably inherited and can influence expression level of genes in the population. Methylation profiles in seedling tissue of a panel of 51 maize inbred lines using a custom 2.1M or 1.4M feature NimbleGen array. Methylation profiles in seedling tissue of maize inbred lines, teosinte and recombinant inbred lines (RILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array. Inbred lines B73 and Mo17 each had 3 biological replicates, the other sample had 1 replicate.
2013-08-12 | E-GEOD-46949 | biostudies-arrayexpress
Project description:The choroid plexus (CP) secretes cerebrospinal fluid and is critical for the development and function of the brain. In the telencephalon, the CP epithelium (CPe) arises from the Wnt- and Bmp- expressing cortical hem. We examined the role of canonical Wnt signaling in CPe development and report that the mouse and human embryonic CPe expresses molecules in this pathway. Either loss of function or constitutive activation of β-catenin, a key mediator of canonical Wnt signaling, causes a profound disruption of mouse CPe development. Loss of β-catenin results in a dysmorphic CPe, while constitutive activation of β-catenin causes a loss of CPe identity and a transformation of this tissue to a hippocampal-like identity. Aspects of this phenomenon are recapitulated in human embryonic stem cell (hESC)-derived organoids. Our results indicate that canonical Wnt signaling is required in a precisely regulated manner for normal CP development in the mammalian brain.
2021-11-01 | GSE162784 | GEO