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Genome wide map of SOX1 occupancy in human embryonic stem cell derived neural progenitors

ABSTRACT: Genome wide map of SOX1 occupancy in human embryonic stem cell derived neural progenitors

PROVIDER: PRJNA575044 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10207419.fastq.gz	Fastqsanger.gz
	SRR10207420.fastq.gz	Fastqsanger.gz
	SRR10207421.fastq.gz	Fastqsanger.gz
	SRR10207422.fastq.gz	Fastqsanger.gz
	SRR10207423.fastq.gz	Fastqsanger.gz

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Genome wide map of SOX1 occupancy in human embryonic stem cell derived neural progenitors

Project description:To understand how SOX1's binding profile in neural progenitor with different regional identities, we differentiated hESC into neural progenitors with rostral and caudal identies throught modulating Wnt signaling pathway. We collected cells at neural differentiation day 4 and 8, and performed SOX1 ChIP-seq to investigate SOX1's genome wide binding profiles. These results provide important information for the mechanism underlying SOX1's functions in early regionalization.

2020-08-26 | GSE138215 | GEO

SOX1 Determines the Regional Identity of Neural Progenitors Differentiated from Human Embryonic Stem Cells

Project description:During human embryogenesis, primitive neural cells start to be generated at the time of gastrulation and gradually acquire regional identities, which is a process called neural patterning. But how intrinsic factors respond to exogenous patterning signals remains poorly understood. Human Embryonic Stem Cells (hESCs) provide a great model to recapitulate this process. Through exogenous manipulation of canonical WNT signaling activation during neural differentiation, dose-dependent specification of regionally defined neural progenitors ranging from the telencephalic forebrain to posterior hindbrain could be rapidly and efficiently induced. Unexpectedly, we find that SOX1, generally referred as a pan-neural gene, displays a regional specific distribution in the human neural patterning process. To investigate the expression and function of SOX1 efficiently, we have generated the SOX1-EGFP reporter and SOX1-knockout (KO) hESC lines using the CRISPR/Cas9 system. SOX1 is initially expressed across the mes–met border and peaked in the metencephalon region at the early regional specification stage. Its depletion leads to the posterior shift of the mes–met border. Therefore, SOX1 is required to define the border at a correct region. In-depth analysis of SOX1 ChIP-sequencing and transcriptome data will provide more insights into how SOX1 determines the mes-met border formation and identify the downstream targets of SOX1. This study identifies SOX1 as one of the intrinsic factors key for the prepattern establishment in the developing central nervous system, particularly for defining the isthmus position.

2020-08-26 | GSE138217 | GEO

RNAseq Data of Neural Stem Cells, Glial progenitors and Sox1 positive Glial progenitors

Project description:With this study we aimed to characterize the changes invoked in glial progenitor cells by activation of the endogenous copy of the master transcription factor Sox1. For this study, a progenitor cell line was derived from ES cells carrying a heterozygous GFP knock-in in the Sox1 ORF. Sox1 positive cells were identified by GFP expression, and separated by FACS. As control population, Sox1 negative progenitors were used, as well as GFP sorted and unsorted, Sox1 positive Neuroepithelial cells derived from the same ES cell line.

2019-04-18 | GSE119480 | GEO

RNAseq Data of Neural Stem Cells, Glial progenitors and Sox1 positive Glial progenitors

Project description:RNAseq Data of Neural Stem Cells, Glial progenitors and Sox1 positive Glial progenitors

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SOX1 is required for the specification of rostral hindbrain neural progenitor cells from human embryonic stem cells

Project description:Region-specific neural progenitor cells (NPCs) can be generated from human embryonic stem cells (hESCs) through modulating signaling pathways. However, how intrinsic transcriptional factors contribute to the neural regionalization are not well characterized. Here, we generate region-specific NPCs from hESCs and find that SOX1 is highly expressed in NPCs with the rostral hindbrain identity. Moreover, we find that OTX2 inhibits SOX1 expression, displaying exclusive expression between the two factors. Furthermore, SOX1 knockout (KO) leads to up-regulation of midbrain genes and down-regulation of rostral hindbrain genes, indicating that SOX1 is necessary for specification of rostral hindbrain NPCs. Our SOX1 ChIP-sequencing analysis reveals that SOX1 binds to the distal region of GBX2 to activate its expression. Overexpression of GBX2 largely abrogates SOX1-KO induced aberrant gene expression. Taken together, this study uncovers previously unappreciated role of SOX1 in early neural regionalization and provides new information for the precise control of the OTX2/GBX2 interface.

2020-08-26 | GSE138218 | GEO

SOX1 Determines the Regional Identity of Neural Progenitors Differentiated from Human Embryonic Stem Cells

Project description:SOX1 Determines the Regional Identity of Neural Progenitors Differentiated from Human Embryonic Stem Cells

| PRJNA575045 | ENA

Transcription profiling of mouse embryonic stem cells differentiated into Sox1 positive neural stem cells. Nap1l2 deleted neural stem cells were compared to nondeleted neural stem cells

Project description:Embryonic stem cells were differentiated into Sox1 positive neural stem cells. Nap1l2 deleted neural stem cells were compared to nondeleted neural stem cells.

2007-12-31 | E-MEXP-1002 | biostudies-arrayexpress

Sox2 ChIP-seq in hindbrain and spinal cord neural progenitors differentiated from mouse embryonic stem cells

Project description:Sox2 is a key determinant of neural cell identity, expressed in neural progenitors from anterior to posterior levels. We asked if the occupancy of this factor changes in neural progenitors with different axial identities. To this end, we performed the directed differentiation of mouse embryonic stem cells to generate neural progenitors in vitro with either hindbrain or spinal cord identity. We then performed Sox2 ChIP-seq (antibody SC-17320X), to assess the difference in Sox2 occupancy at these two different axial levels. This revealed that the genome-wide occupancy of Sox2 in neural progenitors changes depending on axial identity.

2018-08-27 | E-MTAB-6348 | biostudies-arrayexpress

Expression data from the adult hippocampus of Sox1-GFP mice

Project description:The dentate gyrus of the hippocampus continues generating new neurons throughout life. These nerve cells originate from radial astrocytes within the subgranular zone (SGZ). We find that Sox1, a member of the SoxB1 family of transcription factors, is expressed in a subset of radial astrocytes. Lineage tracing using Sox1 driven reporter mice shows that the Sox1-expressing cells represent an activated neural stem/progenitor population. We used microarrays to evaluate the molecular constitution of neural stem cells with aging.

2012-08-09 | GSE39992 | GEO

Transcription profiling of human embryonic stem cells during differentiation to more restricted neural progenitors

Project description:The purpose of this study was to examine global gene expression during the differentiation of human embryonic stem cells to more restricted neural progenitors. We developed an adherent differentiation protocol with completely defined media that produced 2 distinct classes of neuroepithelia based on timing, morphology and expression of known neural markers. The first stage of differentiation is undifferentiated human ES cells (hESCs). The second stage is aggregates of these hESCs after 6 days of separation from supportive mouse embryonic fibroblasts. The third stage is a primitive anterior neuroepithelia that arises after 10 days of differentiation and is marked by a columnar morphology, expression of Pax6 and anterior neural patterning genes. The fourth stage peaks at 17 days when cells form rosettes that resemble the neural tube and express the pan-neural marker Sox1.

2007-03-09 | E-SMDB-3806 | biostudies-arrayexpress

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