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RNA-Seq of developing shoot apical meristems of barley cultivar Bonus and two allelic praematurum-c/mat-c mutants mat.c.907 (NGB 116862) and mat.c.943 (NGB 117474) grown under long- and short-day photoperiods

ABSTRACT: RNA-Seq of developing shoot apical meristems of barley cultivar Bonus and two allelic praematurum-c/mat-c mutants mat.c.907 (NGB 116862) and mat.c.943 (NGB 117474) grown under long- and short-day photoperiods

PROVIDER: PRJEB31822 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3239120.fastq.gz	Fastqsanger.gz
	ERR3239130.fastq.gz	Fastqsanger.gz
	ERR3239140.fastq.gz	Fastqsanger.gz
	ERR3239150.fastq.gz	Fastqsanger.gz
	ERR3239160.fastq.gz	Fastqsanger.gz

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RNA-Seq of developing shoot apical meristems of barley cultivar Bonus and two allelic praematurum-c/mat-c mutants mat.c.907 (NGB 116862) and mat.c.943 (NGB 117474) grown under long- and short-day photoperiods

Project description:Natural variation in the barley homolog of CENTRORADIALIS (HvCEN), was found to contribute to the expansion of barley cultivation into diverse habitats. It has been shown that induced hvcen mutants, originally designated as praematurum-c/maturity-c (mat-c) mutants, flowered a few days earlier under natural long-day conditions. All hvcen mutants flowered early and showed a reduction in spikelet number per spike, tiller number and yield in the outdoor experiments. Further evaluating development of main shoot apex of hvcen mutants and wild type under controlled long day and short day conditions showed that mutations in hvcen accelerated spikelet initiation and reduced axillary bud number in a photoperiod independent manner, but promoted floret development only under long days. In this project we investigate the pleiotropic effects of HvCEN on developmental timing and shoot and spike morphologies of barley and dependence on these effects on photoperiod. This RNAseq dataset was generated to identify the putative transcriptional targets of HvCEN. To this end, we used global transcriptome profiling in developing shoot apices and inflorescences of two allelic hvcen mutants (mat-c.907 and mat-c.943) and wild-type (Bonus) plants grown under long- and short-day photoperiods.

2019-04-23 | E-MTAB-7807 | biostudies-arrayexpress

Genome-wide Gene Expression Profiling in DLBCL Cell Lines Treated with CUDC-907

Project description:CUDC-907 is a small-molecule dual-acting inhibitor of HDACs and PI3Ks, which effectively suppresses the growth and survival of MYC-altered DLBCL. To evaluate the effect of CUDC-907 on MYC-associated genes, two DLBCL cell lines were treated with CUDC-907, a total of 948 differentially regulated genes were identified. 24 genes from the CUDC-907–regulated 948-gene set present either in the "HALLMARK_MYC_TARGETS_V1” 200-gene set or in the “HALLMARK_MYC_TARGETS_V2” 58-gene set in the Molecular Signatures Database (MSigDB). We then computed the correlation coefficients (r) between gene expression levels and MYC protein levels across all samples in the TCGA DLBCL dataset. We found that mRNA expression changes induced by CUDC-907 in the two DLBCL cell lines are negatively correlated with correlation coefficients between expression levels and MYC protein level in the TCGA DLBCL dataset

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Blitum bonus-henricus

Project description:Blitum bonus-henricus overview

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Neuroglobin (Ngb) Knockdown effect on glioblastoma cell line G422.

Project description:The aim was to identify genes that were influenced by Ngb Knockdown in glioblastoma cell lines.

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E-MTAB-7807

Project description:RNA-Seq of developing shoot apical meristems of barley cultivar Bonus and two allelic praematurum-c/mat-c mutants mat.c.907 (NGB 116862) and mat.c.943 (NGB 117474) grown under long- and short-day photoperiods

2019-09-09 | E-MTAB-7807 | ExpressionAtlas

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Project description:Purpose: Hepatic stellate cells (HSCs) plays an important role in liver fibrosis. MB and NGB can inhibit the activation of HSCs. The goal of this study is to investigate the MB and NGB targeted signalling pathways regulating the activation of HSCs. Method: mRNA profiles of HHSteCs control, HHSteCs treated with MB (4 µM, for 48 hour), and HHSteCs treated with NGB (4 µM, for 48 hour) were generated by deep sequencing. Results: The RNA-seq data confirmed that extracellular matrix-encoding genes and fibrosis-related genes were down-regulated by the MB and NGB treatment.

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Gene expression profile of control and NGB knockdown human cerebral organoids at day 65.

Project description:We use single cell RNA sequencing (scRNA-seq) to analyze the impact of NGB on early neural development based on cerebral organoids model.

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Effect of acute and chronic 7% O2 hypoxia on gene expression in the brain of Ngb-null mice

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SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes [ChIP-seq]

Project description:The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus’s repressive activity. SUMOylation influences Bonus’s subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.

2023-08-26 | GSE241372 | GEO

Gene expression profile of control and NGB knockdown human cerebral organoids at day 24 and 35

Project description:We use single cell RNA sequencing (scRNA-seq) to analyze the impact of NGB on early neural development based on cerebral organoids model.

2025-03-19 | GSE253940 | GEO

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