Condylostoma magnum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA263178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1606223.fastq.gz | Fastqsanger.gz | |||
| SRR1606223_1.fastq.gz | Fastqsanger.gz | |||
| SRR1606223_2.fastq.gz | Fastqsanger.gz | |||
| SRR1614990.fastq.gz | Fastqsanger.gz | |||
| SRR1614990_1.fastq.gz | Fastqsanger.gz |
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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.
2021-03-22 | GSE123588 | GEO
Project description:Bifidobacterium magnum DSM 20222
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Project description:Broiler chicken production is crucial to meet the increasing global food demand. Hyperphagic and obese broiler breeder hens have a short production cycle, which is challenged by age-associated egg quality and fertility decline, affecting hatchability. A fertilized egg is a comprehensive set of essential elements to nurture and develop a healthy chick. Egg albumin occupies most of the egg content, which is synthesized and secreted by the magnum. The genetic regulation of albumin biosynthesis in broiler breeder hens and its alteration with age might reveal the genetic marker that will produce quality eggs in subsequent generations. Hence, the objective of the study is to determine the differentially expressed genes (DEGs) and pathways involved in albumin biosynthesis in the magnum (young vs aged). The magnum tissues were collected from the broiler breeder hens at peak production, identified as the young group (35 weeks, N=30), and from the declined production, recognized as the aged group (50 weeks, N=30). Five samples from each group (n=5) were used for RNA sequencing and analyzed to get DEGs and associated pathways. The significantly upregulated genes with a putative function in quality egg formation were confirmed using qPCR. Seventy-five up-regulated and 52 down-regulated genes were determined. The top 20 most upregulated genes and top 20 most downregulated genes, based on their putative function, were categorized into five groups: egg white synthesizing (AMDHD1, FER, CTNNA3), molecular communication (VAPA), oviduct tissue regeneration (ADAM19, CFAP100, AMD1, TM4SF19, SLC39A13, VMO1), and defense (ZBTB46, STAM2, OVoDA3). “Post-translational protein phosphorylation” was the most significantly enriched Reactome pathway involving DNAJC3, PPP3CA, TF, SPARCL1, PDIA6, SGPP2, HSP90B1, and PNPLA2 genes. The study successfully identified DEGs, genetic networks, and pathways that can be used as genetic markers to select quality egg producing broiler breeder hens.
2025-05-16 | GSE296459 | GEO
Project description:Sulfate-reducing bacteria (SRB) play a pivotal role in the global carbon- and sulfur cycles, especially in the marine environment. Here, continental margins, coastal ranges, and shelf sediments stand out by their high input of organic matter, and more than 50% of their mineralization is achieved in the upper sediment layers, coupled to sulfate reduction. This turnover is mainly achieved by members of the family of Desulfobacteraceae of completely oxidizing SRB. Desulfonema magnum is a member of this family.
2025-03-11 | PXD053594 | Pride