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To perform a standard RNAseq experiment to evaluate the impact of the knockout of Zeus gene(CG9573) in D. melanogaster

ABSTRACT: To perform a standard RNAseq experiment to evaluate the impact of the knockout of Zeus gene(CG9573) in D. melanogaster

PROVIDER: PRJNA793594 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17400003.fastq.gz	Fastqsanger.gz
	SRR17400004.fastq.gz	Fastqsanger.gz
	SRR17400005.fastq.gz	Fastqsanger.gz
	SRR17400006.fastq.gz	Fastqsanger.gz
	SRR17400007.fastq.gz	Fastqsanger.gz

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To perform a standard RNAseq experiment to evaluate the impact of the knockout of Zeus gene(CG9573) in D. melanogaster

Project description:This experiment was designed to study the transcriptional alternations using RNA-seq technique. RNA materials were collected and sequenced with multiple experimental groups in tri-plicates as follows: control-knockout-replicate 1~3 (KO-Ctrl__1~3), Zeus-knockout-replicate 1~3 (KO-Zeus__1~3), for RNA-sequencing. In total, 6 sequencing files were downloaded from the genomic core facility, University of Chicago. The aims of this analysis are to 1) conduct quality control (QC) assessment on the original raw sequencing data, 2) map sequencing reads to target species, 3) identify differentially expressed (DE) protein-coding genes per comparison. Through assessing the quality of original raw sequencing data, good base-wise quality was revealed in average in all samples, indicating a high confidence on the base call. Adapter/primer sequences are absent from reads; therefore, trimming of sequencing reads was skipped prior to downstream RNA-seq analysis. Overall, around 94.89% of reads were successfully mapped to the fruit fly genome model in RNA-seq data. All RNA samples were used for further downstream identification of differentially expressed (DE) mRNA genes in individual pairwise comparison. Several commonly used tools (DESeq2, edgeR, and limma) were utilized for the identification of DE mRNA between pairwise groups. Using the criteria of fold change no less than 1.5 and FDR (False Discovery Rate) less than 0.1). Pairwise comparison, KO-Zeus/KO-Ctrl, were conducted. Overall, we find Zeus regulated the expression of 661 differentially expressed genes (DEGs) based on combination of three tools. Venn diagram was further depicted to present the consensus/overlapped DE gene sets detected across different methods.

2022-01-04 | GSE192879 | GEO

ASTRAL deep-proteotyping of a human fecal standard to evaluate metaproteomics strategies.

Project description:Metaproteomics of a human fecal standard, MetaP, with ASTRAL tandem mass spectometer operated in data-dependent analysis for deep-proteotyping and evaluate metaproteomics strategies.

2024-03-07 | PXD045838 | Pride

Zeus Caf40 ChIP-chip

Project description:Zeus Caf40 ChIP-chip with FLAG tag in D. melanogaster adult flies

2012-05-01 | GSE36573 | GEO

Recent Cis-Trans Coevolution Driven by the Emergence of A Novel Gene in Drosophila

Project description:Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes (Chen et al. 2013)1. Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome Chen et al. 2012)2. However, the way in which new DNA-binding proteins acquire and co-evolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we find a dynamic pattern in which Zeus binding rapidly co-evolved with a previously unknown DNA motif under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Our results suggest that evolution of young regulatory genes can be coupled to substantial re-wiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic, genome-wide evolutionary processes associated with new genes.

2022-01-04 | GSE192880 | GEO

Jena Experiment: Drought Experiment

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Most Sinorhizobium meliloti ECF-sigma factors perform accessory functions

Project description:Most Sinorhizobium meliloti ECF-sigma factors perform accessory functions

| PRJNA479859 | ENA

Exploris 480 dataset acquired on a human fecal standard to evaluate metaproteomics strategies.

Project description:Metaproteomics of a human fecal standard, MetaP, with an Exploris480 tandem mass spectometer operated in data-dependent analysis for proteotyping and evaluation of metaproteomics strategies.

2024-03-07 | PXD047139 | Pride

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Project description:Immigration Experiment

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Interspecies Pinaceae comparison experiment

Project description:The goal of this experiment is to evaluate the potential for utilising this oligonucleotide microarray in other species and genera of the Pinaceae family by using comparative RNA hybridizations in four different spruces (Picea spp), two pines (Pinus spp.) and a larch (Larix laricina), across two tissues, xylem and phelloderm.

2012-02-16 | GSE35847 | GEO

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Project description:The objective of this experiment was to compare the affect of H3B-5942 treatment on global gene expression and to compare to treatment with standard of care agents tamoxifen and fulvestrant.

2018-06-12 | GSE115609 | GEO

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