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Ikzf2/helios mutant cochlear RNA-seq analysis

ABSTRACT: Given the potential role of the helios transcription factor in postnatal outer hair cell gene regulation indicated by our RiboTag translatome analyses, our next goal was to identify and validate genes that are regulated by helios in outer hair cells by performing RNA-seq on P8 cello mutant animals compared to wild-type littermates.

ORGANISM(S): Mus musculus

PROVIDER: GSE116702 | GEO | 2018/11/28

REPOSITORIES: GEO

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RiboTag translatome analysis of outer hair cell postnatal development

Project description:In order to determine the regulators of outer hair cell postnatal maturation, we utilized the RiboTag mouse model to perform a detailed transcriptomic analysis of outer hair cells at five postnatal developmental time points: P8, P14, P28, 6 weeks (6wk) and 10 weeks (10wk). This analysis resulted in consistent enrichment of outer hair cell expressed genes in the immunoprecipitated RNA compared to whole cochlear input RNA from each time point. Using transcription factor binding motif prediction on a set of defined outer hair cell enriched genes, we further use this dataset to identify the helios transcription factor as a regulator of the postnatal outer hair cell transcriptome.

2018-11-28 | GSE116703 | GEO

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Ikzf2/helios mutant cochlear RNA-seq analysis

Project description:Ikzf2/helios mutant cochlear RNA-seq analysis

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Single cell transcriptional profiles of control and Ikzf2-transfected mouse cochlear cells

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RiboTag analysis of Gfi1Cre/Cre and Gfi1Cre/+ cochlear and vestibular hair cells

Project description:In order to identify the transcriptional cascade downstream of the GFI1 repressor in inner ear hair cells, we performed a RiboTag-based expression analysis of Gfi1cre/cre mutant hair cells compared to their heterozygous controls. Through this analysis, we identified a significant downregulation of genes involved in normal hair cell development and function within the mutant hair cells, suggesting that in the absence of GFI1, the hair cells undergo a maturation arrest. Furthermore, the Gfi1 deficient hair cells displayed a significant upregulation of genes involved in neurodifferentiation and neuronal function.

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Cell-type specific phenotypic characterization of Lyve1+ perivascular macrophages and Sall1+ microglia pooled from PBS and amyloid-β-injected mice

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Project description:It has been known that aberrant isoforms of Ikaros family ptoteins are expressed in malignant cells. We identified that PBMC of ATL (acute T-cell leukemia) patients expresses different patterns of Helios isoforms compared with normal PBMC. In order to investigate the biological impact of ATL-type Helios isoform, we conducted complehensive gene expression analyses in Jurkat cells overexpressing ATL-type Helios. Also, we investigated the influence of WT-Helios or WT-Ikaros knockdown on the gene expression profile and compared with that of the cells with ATL-type Helios overexpression. Total RNA samples from Jurkat cells were subjected to Cy-3 labeling followed by human whole genome gene expression microarray analyses.

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Influence of ATL-type Helios overexpression or WT-Helios/Ikaros knockdown on gene expression profile in Jurkat cells

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