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: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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Project description:Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells.
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Project description:Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. Therefore, we examined the splicing efficiency of plastid and nuclear genes in lefko1 mutant Methods: The lefko1 mutant was isolated from a genetic screen of an M2 EMS-mutagenized Arabidopsis thaliana Columbia (Col-0) background seed population. The lefko1 mutant allele has a white cotyledon phenotype caused by a G to A mutation in the coding region resulting in a Glycine (G) 373 to Aspartic acid (D) conversion. Total RNA was extracted using plant RNA kit spin columns with an on-column DNase treatment from lefko1 mutant and wild-type Arabidopsis cotyledons. The quantity and integrity of the RNA was assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2000 instrument at BGI (Beijing Genomics Institute).Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”. Differential alternative splicing events were detected for lefko1 and wild-type using rMATS and visualized using the Integrative Genomics Viewer (IGV) tool. Results: Splicing defects were observed in numerous nuclear genes of lefko1 cotyledons compared to wild type. Among them, intron retention (IR) events were the most prominent. Further, the fidelity of 5’ splice site (5’SS) donor and 3’SS acceptor splicing was disturbed in lefko1 cotyledons. To less extend, exon skipping (ES) defects were also detected. Conclusions: Detailed nuclear splicing events were widely observed in lefko1 cotyledons demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns. Overall design: RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2500 instrument at BGI (Beijing Genomics Institute). Conclusions: Detailed nuclear splicing events were widely observed in lefko1 cotyledons demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns.
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