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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Zrf1 is required to establish and maintain neural progenitor identity (mRNA array)

ABSTRACT: Our work aims to characterize the role of Zrf1 in the generation and maintenance of neural progenitor cells (NPCs) Gene expression profile of shCtrl and shZrf1 cells during generation of RGC-like NPC from ESC at day 6 of neural induction. Cells were grown according to this protocol: Bibel et al, Nat Prot., 2007

ORGANISM(S): Mus musculus

SUBMITTER: Luciano Di Croce

PROVIDER: E-GEOD-53541 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Zrf1 is required to establish and maintain neural progenitor identity (mRNA array)

Project description:Our work aims to characterize the role of Zrf1 in the generation and maintenance of neural progenitor cells (NPCs)

2013-12-21 | GSE53541 | GEO

Zrf1 is required to establish and maintain neural progenitor identity (ChIP-Seq)

Project description:We report ChIP-seq data for Zrf1 and Ring1B occupancy in NPC Examination and comparison of DNA binding profile of Zrf1 and Ring1B in NPC

2013-12-21 | E-GEOD-53540 | biostudies-arrayexpress

Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

Project description:Id proteins are dominant negative regulators within the HLH family of proteins. In embryonic stem cells (ESCs), Id1 and Id3 maintain the pluripotent state by preventing neural differentiation. The Id1-interacting protein Zrf1 plays a crucial role as a chromatin-bound factor in specification of the neural fate from ESCs. Here, we show that Id1 blocks Zrf1 recruitment to chromatin, thus preventing the activation of neural genes during ESC differentiation. Moreover, genetic deletion of Id1 in ESCs caused misexpression of more than 6000 genes. Interestingly, the expression of almost half of those genes was restored upon further depletion of Zrf1. We therefore identified Zrf1 as a transcriptional regulator downstream of Id1 in ESCs. In Id1KO mESCs, Zrf1 expression was depleted by using shRNAs. Four replicates corresponding to four independent biological samples per group were collected.

2014-11-05 | E-GEOD-58627 | biostudies-arrayexpress

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Genome-wide occupancy of ZRF1 and BRD4 in neuroblastoma cells.

Project description:Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through integrated proteomics and validating studies, we discovered that ZRF1 and BRD4 form a complex with p113, a novel protein derived from CUX1 circular RNA. To investigate the mechanisms underlying the oncogenic functions of ZRF1 and BRD4, we employed the Illumina Novaseq 6000 as a discovery platform to analyze the genome-wide occupancy of ZRF1 and BRD4 on target genes in human SH-SY5Y cells, while the results were further analyzed with p113-regulated target genes. The results showed that 46 target genes were regulated by transcriptional trimer complex p113/ZRF1/BRD4, especially those involved in metabolic pathway or complex I biogenesis, including ALDH3A1, NDUFA1, and NDUFAF5. Furthermore, we validated the ChIP-seq results by real-time PCR with high identity. Overall, our results provided fundamental information about the genomic enrichment of ZRF1 and BRD4 in human NB cells, and these findings will help us understand the pathogenesis of NB.

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Zrf1 is required to establish and maintain neural progenitor identity

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance

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ZRF1 knockdown with shRNA in SK-N-BE(2) cells

Project description:ZRF1 was silenced using two different shRNA in SK-N-BE(2) neuroblastoma cell line

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Arabidopsis thaliana seedlings: Wild type vs. zrf1 mutants

Project description:Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and zrf1 mutants is performed using Agilent's Whole Arabidopsis Gene Expression Microarray (4x44K).

2016-12-31 | GSE76244 | GEO

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