CTCF ChIP-Seq from Primate iPSC derived Astrocytes (iAstrocytes)
Ontology highlight
ABSTRACT: CTCF ChIP-Seq experiment was performed to map and compare potential evolutionary changes of CTCF binding, chimpanzee and macaque iAstrocytes.
Project description:ATAC-seq experiments were performed to map the open chromatin regions of human, chimpanzee and macaque iAstrocytes. This experiment allowed to compare evolutionary changes according to chromatin activity.
Project description:H3K4me3 ChIP-Seq experiment was performed to map and compare potential evolutionary changes in active promoters of human, chimpanzee and macaque iAstrocytes.
Project description:H3K27ac ChIP-Seq experiment was performed to map and compare potential evolutionary changes in active promoters and enhancer elements of human, chimpanzee and macaque iAstrocytes.
Project description:RNA-Seq experiment to detect transcriptional differences in iPSC derived astrocytes between 3 primate species, humans, chimpanzees and macaques. The goal of the experiment is to characterise genome-wide evolutionary changes in transcriptional and regulatory systems across the primate lineage in astrocytes
Project description:Hi-C experiment was performed to map and compare potential evolutionary changes in chromatin structural organisation of human, chimpanzee and macaque iAstrocytes.
Project description:The human brain has changed dramatically from other primate species, but the genetic and developmental mechanisms behind the differences remains unclear. Here we used single cell RNA sequencing based on 10X technology to explore temporal transcriptomic dynamics and cellular heterogeneity in cerebral organoids derived from human and non-human primates chimpanzee and rhesus macaque stem cells. Using cerebral organoids as a proxy of early brain development, we detect a delayed pace of human brain development relative to the other two primate species. Additional human-specific gene expression patterns resolved to different cell states through progenitors to neurons are also found. Our data provide a transcriptomic cell atlas of primate early brain development, and illustrate features that are unique to humans.
Project description:Astrocytes are key regulators of CNS homeostasis and their dysfunction is implicated in neurological and neurodegenerative disorders. Here, we describe a two-step protocol to generate astrocytes from iPSCs using a bankable neural progenitor cell (NPC) intermediate, followed by low-density passaging and overexpression of the gliogenic transcription factor NFIA. A bankable NPC intermediates allows for facile differentiation into both purified neuronal and astrocyte cell types in parallel from the same genetic background, depending on the experimental needs. This article presents a protocol to generate NPCs from iPSCs (Basic Protocol 1), which are then differentiated into iPSC-derived astrocytes, termed iAstrocytes (Basic Protocol 2). The resulting iAstrocytes express key markers of astrocyte identity at transcript and protein levels by bulk RNA-seq and immunocytochemistry respectively. Additionally, they respond to the inflammatory stimuli poly(I:C) and generate waves of calcium activity in response to either physical activity or addition of ATP. Our approach offers a simple and robust method to generate and characterize human astrocytes which can be used to model human disease affecting this cell type.
Project description:We performed an evolutionary comparison of the binding of the TF CTCF in human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines (LCLs). We also probes YY1 binding in human, chimpanzee, orang-utan and baboon LCLs as well as human and mouse liver.