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Hi-C in the Drosophila wild-type embryos at 2-4h after egg-laying

ABSTRACT: Hi-C in the Drosophila wild-type embryos at 2-4h after egg-laying

PROVIDER: PRJEB55154 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10026230_1.fastq.gz	Fastqsanger.gz
	ERR10026230_2.fastq.gz	Fastqsanger.gz
	ERR10026231_1.fastq.gz	Fastqsanger.gz
	ERR10026231_2.fastq.gz	Fastqsanger.gz
	ERR10026232_1.fastq.gz	Fastqsanger.gz

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Hi-C in the Drosophila wild-type embryos at 2-4h after egg-laying

Project description:Hi-C was performed on 2 biological replicates of wild-type Drosophila embryos at 2-4 hrs after egg-laying. Each library was first checked on MiSeq and then deeply sequenced on HiSeq 2000 (4 lanes for each biological replicate)

2023-05-14 | E-MTAB-12070 | biostudies-arrayexpress

Hi-C in the Drosophila wild-type embryos at 6-8 h and 16-18 hrs after egg-laying

Project description:Hi-C was performed on wild-type Drosophila melanogaster embryos at 6-8 hrs and 16-18 hrs after egg-laying, on 2 biological replicates per time point. Each library was first checked on MiSeq and then deeply sequenced on HiSeq 2000 (4 lanes for each biological replicate). This study completes the E-MTAB-12070 Hi-C dataset on 2-4 hrs wild-type Drosophila melanogaster embryos. Both studies use the same experimental procedures (protocols, sequencer model and run parameters)

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Hi-C in the Drosophila wild-type embryos at 6-8 h and 16-18 hrs after egg-laying

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Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide varitey of tissues has discovered. The aim of this study are to perform transcriptome profiling (RNA-seq) of magnum to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Magnum mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least three-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 30.5 million reads from layers and 33.4 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 540 were differentially expressed between layer and non-layer hens. 152 DEGs were significantly up-regulated and 388 were significantly down-regulated in the laying hens when compared to the non-laying hens. Conclusions: Our study reports the expression of several pre-discovered and many novel genes that may be involved in the transport of precurosor molecules for biosynthesis and secretion of the egg-white proteins in the magnum. These genes can be used as quantitative basis of selecting hens with an improved egg quality.

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Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[RNA-Seq]

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PRO-cap in Drosophila melanogaster embryo at 3-4h and 6-8h after egg laying

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