Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data comparing transformed or neoplastic human neural precursors following OTX2 knockdown to transformed human neural precursor cells

ABSTRACT: Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies. We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following knockdown of OTX2 in transformed or neoplastic human embryonic neural precursor cells. OTX2 was knocked down in transformed human embyronic neural precursors (trans-hEN) using Silencer select siRNAs. trans-hEN OTX2 KD and scrambled control trans-hENs were then grown as neurospheres in defined medium and collected at passage 1. RNA was extracted using the Norgen All-in-One kit.

ORGANISM(S): Homo sapiens

SUBMITTER: Tamra Werbowetski-Ogilvie

PROVIDER: E-GEOD-66671 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data comparing OTX2-overexpressing human neural precursors to human neural precursor cells

Project description:Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies. We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following overexpression of OTX2 in human embryonic neural precursor cells. OTX2 was stably overexpressed in human embyronic neural precursors (hEN) by lentiviral transduction. OTX2-hENs and control hENs were then grown as neurospheres in defined medium and collected at passage 2. RNA was extracted using the Norgen All-in-One kit.

2015-08-25 | E-GEOD-66670 | biostudies-arrayexpress

Expression data comparing transformed or neoplastic human neural precursors following OTX2 knockdown to transformed human neural precursor cells

Project description:Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies. We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following knockdown of OTX2 in transformed or neoplastic human embryonic neural precursor cells.

2015-08-25 | GSE66671 | GEO

Expression data comparing OTX2-overexpressing human neural precursors to human neural precursor cells

2015-08-25 | GSE66670 | GEO

Otx2 controls regional patterning within the MGE and regional identity of the septum [ChIP-Seq]

Project description:The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE. Microdissected subpallium (septum, MGE, and LGE ) from wildtype E12.5 CD-1 embryos was used in three independentanti-OTX2 ChIP-seq experiments.

2015-06-10 | E-GEOD-69724 | biostudies-arrayexpress

Otx2 ChIP-seq in the adult mouse Retinal Pigmented Epithelium (RPE) and neural retina

Project description:Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina. WT and GFP antibodies were used to perform two independent ChIP-seq experiments using Illumina GAIIx.

2014-01-15 | E-GEOD-54084 | biostudies-arrayexpress

Adult mouse choroid plexus OTX2 Co-IP

Project description:To analyze OTX2 function in adult choroid plexus, we performed several OTX2 co-immunoprecipitation (co-IP) experiments with mass spectrometry analysis to identify potential protein partners. We previously discovered that OTX2 protein also accumulates non-cell autonomously in subventricular zone (SVZ) and rostral migratory stream (RMS) astrocytes and in visual cortex (VCx) parvalbumin cells. The identification of alternate protein partners in cell-autonomous and non-cell-autonomous contexts would suggest OTX2 takes on specific roles after transferring between cells. In order to test this hypothesis, and to reinforce choroid plexus analysis, we also performed OTX2 co-IP on lysates from adult mouse SVZ, RMS and VCx.

2021-08-23 | PXD021244 | Pride

Otx2 ChIP-seq in the adult mouse Retinal Pigmented Epithelium (RPE) and neural retina

2014-01-15 | GSE54084 | GEO

Otx2 binding to Nanog promoter protects embryonal stem cells from corruption of naive pluripotency and is required at morula stage for inner-cell mass differentiation of the epiblast

Project description:We have investigated the functional relevance of the transcriptional network controlled by the Otx2 binding activity in ESCs, EpiSCs and in vivo. In particular, to study the Otx2 transcriptional network we first performed Otx2 chromatin immunoprecipitation sequencing (ChIP-seq) experiments in wt ESCs and day 4 (d4) ESC-derived EpiSCs and employed as negative control ESCs and EpiSCs lacking Otx2. Moreover, to investigate the functional relevance of the Otx2 binding activity in pluripotent stem cells, we mutagenized in ESCs the Otx2 binding site located upstream of the Nanog TSS. To characterize the identity of ESCs and EpiSCs both lacking this Otx2 binding site, we analyzed their transcriptome by RNA-Seq.

2016-06-09 | E-MTAB-3856 | biostudies-arrayexpress

syangArray

Project description:Gene expression was studied in the presence or absence of Otx2 (RNAi) in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) in undifferentiated and differentiated states.

2014-06-24 | E-MTAB-2239 | biostudies-arrayexpress

syangRNAseq

2014-06-24 | E-MTAB-2245 | biostudies-arrayexpress