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Gene expression changes in 48hr APF retinas and optic lobes in Blimp-1 loss of function and gain of function flies

ABSTRACT: Gene expression changes in 48hr APF retinas and optic lobes in Blimp-1 loss of function and gain of function flies

PROVIDER: PRJNA761775 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15826144_1.fastq.gz	Fastqsanger.gz
	SRR15826144_2.fastq.gz	Fastqsanger.gz
	SRR15826145_1.fastq.gz	Fastqsanger.gz
	SRR15826145_2.fastq.gz	Fastqsanger.gz
	SRR15826146_1.fastq.gz	Fastqsanger.gz

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Gene expression changes in 48hr APF retinas and optic lobes in Blimp-1 loss of function and gain of function flies

Project description:Blimp-1 encodes a zinc-finger transcription factor, which is involved in the terminal differentiation of the Drosophila eye. We found that Blimp-1 mutants display plano-covex corneal lenses and rhabdomere extension defects. To identify genes that it regulates in the retina, we performed an RNA-seq experiemtn to compare retinas expressing Blimp-1 RNAi or UAS-Blimp-1 in all cell types in the eye with lGMR-GAL4 to control lGMR-GAL4/+. We examined RNA from dissected retinas and attached optic lobes from 48 hr APF pupae. Among the genes that were affected, we found that the transcription factor Slow border cells (Slbo) was significantly up-regulated in Blimp-1 knockdown samples, and Slbo overexpression could recapitulate Blimp-1 loss of function phenotypes. Many other affected genes may collectively contribute to the corneal lens and photoreceptor phenotypes caused by loss of Blimp-1..

2022-03-07 | GSE183734 | GEO

miRNA expression in Blimp-1-deficient dendritic cells

Project description:Expression of Blimp-1 was specifically deleted in dendritic cells (DCs) by breeding Blimp-1 flox and CD11c-CRE mice. MiRNA expression was evaluated and compared from DCs, CD4+ T cells and total B cells from spleens of control and Blimp-1 KO mice. Age-matched (6-10 weeks old) female mice from control and Blimp-1 KO mice were sacrificed and spleens were collected. CD11chi/MHCIIhi DCs, CD4+TCRb+ T cells and B220+ B cells were sorted by FACSaria. MiRNA was measured from the total RNA preparation.

2013-09-05 | E-GEOD-40587 | biostudies-arrayexpress

Analysis of Blimp-1 and Irf-1 genomic binding in wild type and Prdm1/Blimp-1 mutant embryonic gut

Project description:The goal of this study was to profile Blimp1 binding in E18.5 small intestine using a Blimp-1-eGFP knock-in allele, and to compare Blimp-1-eGFP genomic binding with Irf-1 genomic binding in normal small intestine. Changes in Irf-1 binding between wild type and Prdm1/Blimp-1 mutant small intestine were also assessed. ChIP-seq was performed for Blimp-1-eGFP in duplicate in E18.5 small intestine expressing the fusion protein using anti-GFP antibody. As a negative control a single anti-GFP ChIP was also performed in wild type small intestine. ChIP-seq for Irf-1 was performed in duplicate in both wild type and Prdm1/Blimp-1 mutant E18.5 small intestine using an anti-Irf-1 antibody. Duplicate IgG ChIP control in wild types was performed as a negative control. All samples had an associated input chromatin sample sequenced.

2015-07-10 | E-GEOD-66069 | biostudies-arrayexpress

miRNA expression in Blimp-1-deficient dendritic cells

2013-09-05 | GSE40587 | GEO

Analysis of Blimp-1 and Irf-1 genomic binding in wild type and Prdm1/Blimp-1 mutant embryonic gut

2015-07-10 | GSE66069 | GEO

Drosophila Sex Hierarchy Regulated Gene Expression in 48 hour APF Pupae

Project description:Drosophila melanogaster undergoes a complete metamorphosis, during which time the larval male and female forms transition into sexually dimorphic, reproductive adult forms. To understand this complex morphogenetic process at a molecular-genetic level, we performed whole genome microarray analyses. In somatic tissues at 48 hour After Puparium Formation (APF), 173 sex-biased transcripts that likely function downstream of the doublesex (dsx) branch of the sex determination hierarchy were identified. The mode of regulation of the sex-specific isoforms of DSX (DSX-F and DSX-M) was examined. It was determined that for most downstream targets, DSX-F and DSX-M regulate gene expression in the same manner, but that one isoform acts as a more potent regulator. Keywords: wild type; genetic modification All microarrays were dual channel with direct comparisons of male versus female or wild type versus mutant. All samples consist of whole body pupae collected at 48 hour After Puparium Formation (APF). For each experiment, four biological replicates were analyzed in a dye-swap design.

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Epigenetic modifications induced by Blimp-1 regulate CD8+ T cell memory progression during acute virus infection

Project description:Blimp-1 regulates the overall accumulation of virus-specific CD8+ T cells during acute viral infections. Increased proliferation and survival of Blimp-1-deficient CD8+ T cells is promoted by persistent cytokine responsiveness, resulting from sustained expression of CD25 and CD27. Knockdown of these genes reduced the Blimp-1-deficient CD8+ T cell response. Genome-wide ChIP-sequencing analysis identified CD25 and CD27 genes as direct targets of Blimp-1. At the peak of the anti-viral response, but not earlier, Blimp-1 recruited the histone modifying enzymes G9a and HDAC2 to the Il2ra and Cd27 loci, thereby repressing expression of these genes. In the absence of Blimp-1, the Il2ra and Cd27 genes exhibited enhanced histone H3-acetylation and reduced histone H3K9-trimethylation. These data elucidate a central mechanism by which Blimp-1 acts as an epigenetic regulator, enhancing the numbers of short-lived effector cells while suppressing the development of memory precursor CD8+ T cells. NaM-CM-/ve CD8+ T cells from OT-I TCR transgenic Rag1-/- mice were stimulated with anti-CD3 and anti-CD28 for three days in vitro, in the presence of IL-2 to up-regulate Blimp-1 protein. Genome-wide mapping of Blimp-1 binding in mouse CD8+ T cells was conducted.

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Drosophila L3 ATAC-seq at 24h APF

Project description:Drosophila L3 ATAC-seq at 24h APF

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Drosophila L3 RNA-seq at 24h APF

Project description:Drosophila L3 RNA-seq at 24h APF

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Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas

Project description:Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control- with 4-OHT-treated. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRÎ²), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of 4-OHT-induced degeneration of photoreceptor cells in the 3D-retinas. 4-OHT-induced gene expression in the 3D-retinas was measured at DD 26 when the photoreceptor cells were degenerated. Two-condition experiment, vehicle control- vs. 5 ÂµM 4-OHT-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1 replicate.

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