Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391840 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5755256_1.fastq.gz | Fastqsanger.gz | |||
| SRR5755256_2.fastq.gz | Fastqsanger.gz |
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Project description:Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by pre-slaughter stress or no stress treatment in pigs of different breed (Italian Duroc, Italian Large White or Pietrain) and differnt Halothane genotype (RYR1 locus CC-NN, CT-Nn or TT-nn) in Pietrain pigs.
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Project description:Pig breeds have different attitude to traits like growth rate, carcass composition and reproduction parameters as well as other traits. These traits considered as external traits or end phenotypes are the outcome of complex biological processes and interactions. The main goal of pig breeding programs and the basis for crossbreeding is finding a balance between these traits. In pig production, Large White and Duroc breeds are commonly used to optimise respectively fertility and growth ability and differ on several production traits, indeed the first breed as a high fertility characters whereas Duroc is used as terminal sire for her growth performance and good carcass quality traits. In this study, we have used a quantitative label-free LC-MS proteomics approach to characterise and compare the liver proteome of two heavy Italian pig breeds, Italian Duroc and Italian Large White to identify difference due to their different genetic background. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 703094.
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Project description:Purpose: this study is to analyze the change of RNA splicing events after disruption of Protein Arginine Methyltranferase 5 (PRMT5) in Plasmodium falciparum. Methods: In this study, the transcriptomes of a PfPRMT5 gene knockout (KO) parasite line with its wildtype control were analyzed by RNAseq.Total RNA were harvested from the asexual parasites at four stages (ring, early trophozoite, late trophozoite, and schizont)(12h, 24h, 36h, and 46h post-invasion) using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2. Results: This RNAseq analysis with strand-specific mRNA libraries from both ΔPfPRMT5 and WT lines showed that >90% of sequencing reads were of high quality for mapping to the P. falciparum genome with nearly 40 times of coverage. This allows us to analyze the change of alternative splicing events (alternative 5' splice site, alternative 3' splice site, retained intron and skipped exon). 800, 1056, 479, and 1158 alternative splicing events (alternative 5' splice site, alternative 3' splice site, retained intron and skipped exon) were altered in the DPfPRMT5 parasite line as compared to the WT line at four development stages, respectively (unpublished data). Conclusions: Collectively, this RNAseq provide a dataset for analysis of abnormal RNA splicing events in the ΔPfPRMT5 parasites.
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Project description:Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by pre-slaughter stress or no stress treatment in pigs of different breed (Italian Duroc, Italian Large White or Pietrain) and differnt Halothane genotype (RYR1 locus CC-NN, CT-Nn or TT-nn) in Pietrain pigs. All 36 samples were hybridised together with a common reference.
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Project description:Pathogenic variants in splicing factors are the second most common cause of autosomal dominant retinitis pigmentosa (RP), with mutations in PRPF31 being the most prevalent. Here, we characterize a novel intronic variant in PRPF31 (c.1074-11C>G) that creates a cryptic 3′ splice site, resulting in an aberrantly spliced transcript predicted to encode a protein with an altered C-terminus. However, the pathogenic protein was not detected in patient-derived induced pluripotent stem cells (iPSCs). In addition, expression of PRPF31 protein was reduced in patient iPSC-derived retinal pigment epithelium (RPE). To correct the splicing defect, we designed a panel of antisense oligonucleotides (ASOs) targeting putative RNA-binding sites in exon 10 and intron 10 and identified a candidate that corrects PRPF31 splicing in a minigene reporter system as well as in patient-derived iPSCs and RPE. Finally, we showed that ASO treatment enhances PRPF31 protein expression in patient iPSC-derived RPE, supporting its potential as a therapeutic approach to restore PRPF31 expression in RP patients.
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Project description:Purpose: We identify the genetic cause of autosomal dominant congenital cataract in a large family and to define how a CRYBB2 splice-site variant perturbs lens development and associated ocular phenotypes. Methods: Whole-exome sequencing and Sanger sequencing were used for variant identification and segregation. Wild-type (WT) or mutant CRYBB2 was expressed in lens epithelial cells to assess splicing and downstream transcriptional changes by RNA sequencing and qRT-PCR. Extracellular matrix (ECM) organization and cell–matrix interactions were examined by immunostaining and adhesion assays. In zebrafish, crybb2 disruption was evaluated using lens structural assays, hyaloid vasculature imaging in Tg(flk1:EGFP) larvae, tracer distribution assays, and mRNA rescue. Single-cell RNA sequencing at 48 hpf was performed to profile lens and vascular populations and infer pathway-level changes. Results: We identified a novel CRYBB2 splice-site variant in affected members of a family with congenital cataract, consistent with an association with the disease in this pedigree. The variant disrupted normal splicing and was associated with altered βB2-crystallin–linked transcriptional programs and ECM homeostasis, including changes in collagen IV/laminin deposition and impaired cell–matrix adhesion. In zebrafish, crybb2 disruption caused lens fiber cell differentiation defects and was accompanied by abnormal hyaloid vascular patterning and altered tracer distribution around the lens; these phenotypes were partially improved by crybb2 mRNA rescue. Single-cell transcriptomic analyses suggested coordinated changes in ECM and junction/adhesion-related pathways across lens and vascular compartments, consistent with a lens-associated, non-cell-autonomous influence on adjacent vasculature. Conclusions: A novel CRYBB2 splice-site mutation is associated with autosomal dominant congenital cataract and disrupts lens homeostasis with accompanying changes in hyaloid vascular remodeling. These findings expand the pathogenic spectrum of CRYBB2 and support a model in which lens abnormalities are associated with altered lens–vascular interactions during development.
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Project description:The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.
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