Sequentially acting Sox transcription factors in neural lineage development [RNA-seq]
ABSTRACT: We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation Loss of function experiment for Sox2/Sox3 in neural progenitor cells and gene expression profile for Sox11 expressing (PSA NCAM sorted) early formed neurons.
Pluripotent embryonic stem (ES) cells can generate all cell types, but how cell lineages are initially specified and maintained during development remains largely unknown. Different classes of Sox transcription factors are expressed during neurogenesis and have been assigned important roles from early lineage specification to neuronal differentiation. Here we characterize the genome-wide binding for Sox2, Sox3, and Sox11, which have vital functions in ES cells, neural precursor cells (NPCs), and ...[more]
Project description:This SuperSeries is composed of the following subset Series: GSE33059: Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq] GSE33060: Sequentially acting Sox transcription factors in neural lineage development [RNA-seq] GSE33061: Sequentially acting Sox transcription factors in neural lineage development [microarray] Refer to individual Series
Project description:We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation Examination of genome-wide Sox2, Sox3 and Sox11 transcription factor binding during different stages of neurogenesis.
Project description:Evaluation of TRAP-sequencing by comparing transcriptomes and translatomes of different organs and distinct cell populations. E14.5 brain and kidney transcriptome and translatome profiling of organs or distinct cell populations from these organs was performed using the Illumina TruSeq RNA technology.
Project description:We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation We used microarray to examine the molecular function of Sox3 in neural progenitor cells. Over-expression of Sox3 under Nestin-promoter in neural progenitor cells. Cells are transgenic for GFP in Sox1 locus and were FACS sorted to obtain pure populations.
Project description:Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells. Cells of four different origins were profiled using commercial SMARTer and compared to five variants of an improved protocol (Smart-Seq2).
Project description:Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) from three independent tonsil donors. Sequencing libraries were prepared from FACS sorted individual ILCs with the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013)
Project description:SOX3 is highly expressed in neural progenitor cells (NPC) within the developing mouse cetral nervous system. A ChIP-Seq experiement was performed for SOX3 in NPCs derived from embryonic stem cells. Identification of SOX3 binidng sites from 3 independent ChIP-seq samples in NPCs
Project description:In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individual cells, from zygote to the cells of the late blastocyst, and also individual cells from the adult liver. Using first generation crosses between two distantly related mouse strains, CAST/Ei and C57BL/6, we determined the expression separately from the maternal and paternal alleles. We found that half of the genes were expressed by only one allele, randomly so that some cells would express the paternal allele, some the maternal and a few cell both alleles. We also observed the spread of the progressive inactivation of the paternal X chromosome. First generation mouse strain crosses were used to study monoallelic expression on the single cell level
Project description:We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells. We generated RNA-Seq libraries for dilution series of MAQC reference RNA and mouse brain RNA to assess technical reproducibility, and for a variety of individual cells including putative circulating tumour cells.
Project description:Notch signaling is an important regulator of stem cell differentiation. All canonical Notch signaling is transmitted through the DNA-binding protein CSL and hyperactivated Notch signaling is associated with tumor development; thus it may be anticipated that CSL deficiency should reduce tumor growth. In contrast, we report that genetic removal of CSL in breast tumor cells caused accelerated growth of xenografted tumors. Loss of CSL unleashed a hypoxic response during normoxic conditions, manifested by stabilization of the HIF1± protein and acquisition of a polyploid giant-cell, cancer stem cell-like, phenotype. At the transcriptome level, loss of CSL upregulated more than 1750 genes and less than 3% of those genes were part of the Notch transcriptional signature. Collectively, this suggests that CSL exerts functions beyond serving as the central node in the Notch signaling cascade and reveals a novel role for CSL in tumorigenesis and regulation of the cellular hypoxic response. CSL +/+ and CSL -/- MDA-MB-231 were subjected to Notch activation/inhibition and xenograft experiment. Total RNA were extracted from the samples and sent to NGS. Single Cell RNA-sequencing was also performed from cells isolated from xenograft tumors.