Ontology highlight
ABSTRACT:
PROVIDER: PRJNA627801 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11602478_1.fastq.gz | Fastqsanger.gz | |||
| SRR11602478_2.fastq.gz | Fastqsanger.gz | |||
| SRR11602479_1.fastq.gz | Fastqsanger.gz | |||
| SRR11602479_2.fastq.gz | Fastqsanger.gz |
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Project description:We used a transcriptomic approach based on the comparison of the expression in the uterine tissue when an hard-shelled egg was in calcification (normal) versus uterine tissue collected after premature expulsion of the egg before mineralization has begun (expelled) to better appreciate which uterine chicken proteins are associated with the supply of minerals and potentially actives on the biomineralisation process during eggshell formation.
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Project description:We used a transcriptomic approach based on the comparison of the expression in the uterine tissue when an hard-shelled egg was in calcification (normal) versus uterine tissue collected after premature expulsion of the egg before mineralization has begun (expelled) to better appreciate which uterine chicken proteins are associated with the supply of minerals and potentially actives on the biomineralisation process during eggshell formation. A total of 16 microarray slides were used for hybridization of the 8 uterine tissues collected when an hard-shelled egg was in calcification (normal), and mixed to the 8 uterine tissues collected after premature expulsion of the egg before mineralization has begun (expelled) were analysed, with an experimental design in dye swap (all the slides labeled with fluorophore Alexa 555 and with Alexa 647 for each condition).
2013-12-10 | E-GEOD-52823 | biostudies-arrayexpress
Project description:Uterine glands and, by inference, their secretions impact uterine receptivity, blastocyst implantation, stromal cell decidualization, and placental development. Changes in gland function across the menstrual cycle are impacted by steroid hormones, estrogen and progesterone, as well as stroma-derived factors. Using an endometrial epithelial organoid (EEO) system, transcriptome and proteome analyses identified distinct responses of the EEO to steroid hormones and prostaglandin E2 (PGE2). Notably, steroid hormones and PGE2 modulated the basolateral secretion of EEO proteins, where cystatin C (CST3) was significantly increased by progesterone and PGE2. CST3 treatment of decidualizing stromal cells significantly decreased the decidualization markers PRL and IGFBP1. The attenuation of stromal cell decidualization via CST3 suggests a role for uterine gland-derived proteins in controlling the extent of decidualization. These findings provide evidence that uterine gland-derived factors directly impact stromal cell decidualization, which has strong implications for better understanding pregnancy establishment and female fertility in humans.
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Project description:Factors delivered to offspring in colostrum within two days of birth support neonatal porcine uterine development. The uterine mRNA transcriptome is affected by age and nursing during this period. Whether uterine microRNA (miRNA) expression is affected similarly is unknown. Objectives were to: 1) determine effects of age and nursing on porcine uterine miRNA expression between birth and postnatal day (PND) 2 using small RNA sequencing (smRNA-Seq) and; 2) define affected miRNA-mRNA interactions and associated biological processes using integrated target prediction analysis.
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Project description:Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.
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Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide variety of tissues has been discovered. The aim of this study are to perform uterine transcriptome profiling (RNA-seq) 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: Uterine 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 two-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 32 million reads from layers and 28 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 616 were differentially expressed between layer and non-layer hens. 229 DEGs were significantly up-regulated and 286 were significantly down-regulated in the laying hens when compared to the non-laying hens. Twelve candiate genes, linked to calcium remodeling, were identified by gene function analysis and validated using qPCR. MEPE, CALCB, OTOP2, STC2 and ATP2C2 were confirmed to be highly expressed in laying hens as compared to molting and non-laying hens. RNA-seq and qPCR data for relative gene expression were highly correlated (R2 =0.99). Conclusions: Our study reports the expression of four novel genes that are speculated to transport calcium ions across the uterine epithellium for eggshell mineralization. These genes can be used as quantitative basis of selecting hens with an improved eggshell quality.
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