Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1054086 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27242477.fastq.gz | Fastqsanger.gz | |||
| SRR27242477_1.fastq.gz | Fastqsanger.gz | |||
| SRR27242477_2.fastq.gz | Fastqsanger.gz | |||
| SRR27242478.fastq.gz | Fastqsanger.gz | |||
| SRR27242478_1.fastq.gz | Fastqsanger.gz |
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Project description:Goal: High-throughput sequencing-by-synthesis (Illumina) RNA sequencing technology was carried out with an aim to gain deeper understanding of immune host protective mechanisms. Here, RNA-seq was applied to understand the differential gene expression profile of mice spleen following immunization with Brucella abortus S19∆per mutant (perosamine synthetase gene mutant of Brucella abortus S19) in comparison to mock immunized mice spleen (PBS inoculated). Methods: RNA-seq data of 15th day post immunized mice spleen (with Brucella abortus S19∆per) and PBS control mice were generated by deep sequencing ( in duplicate) using IlluminaNextSeq 500 . The sequence reads that passed quality filters were analyzed for transcript abundance using RSEM package (RNA-Seq by Expectation Maximization) (Li and Dewey, 2011). Breifly, the RSEM package generated a reference sequence based on given mouse transcript annotations (Mus_musculus.GrCm38.83.chr.gtf.gz). The Bowtie allignmet tool available within the package was used to calculate expected counts (number of mapped reads) using quality trimmed reads and reference sequence. Finally, the expected counts estimated by RSEM were fed into different DE package tools, such as DESeq2 (Love et al., 2014), edgeR (Robinson et al., 2010) and EBSeq (Leng et al., 2013) in order to identify differentially expressed genes across spleen samples (B. abortus S19∆per versus (vs) PBS control. Functional annotation of differently expressed genes were carried out using g:Profiler (Reimandet al., 2016; http://biit.cs.ut.ee/gprofiler/). Results: A mean of 37.58 million processed reads (range: 30.51 million to 51.79 million reads per individual RNA-seq library) were generated during the experiment. The expected counts generated by the RSEM package followed by differential analysis calculation using different DE packages identified a total of 1917 differentially expressed genes (DEGs), of which 968 and 949 genes were up- and down-regulated respectively. Functional annotation revealed 545 significantly enriched genes to be associated with immune system processes within the total 1917 differentially expressed genes. Further analysis revealed 21 genes showing significant expression were also in MHC-I and MHC-II antigen processing and presentation pathway during S19∆per immunization. Conclusions:The RNA-seq data revealed the coordinated up-regulation of MHC-I and MHC-II processing pathways providing insights into the molecular mechanism of immune protection conferred by B. abortus S19∆per in mice at day 15 post immunization and might aid in the development of new attenuated vaccine strains with improved efficacy.
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Project description:The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here, we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. reference genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 ribosomal DNA(rDNA) units. Genome-wide rearrangements, centromeric elements, TE expansion, and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, TE insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence (HC) protein-coding genes. However, in such a hexaploidy genome, 20.05%, 33.43%, and 42.76% of gene transcript levels, alternative splicing events, and protein levels were detected unbalancing among subgenomes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity, and provides insights for future wheat research and breeding.
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Project description:Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics. Genome evolution influences a parasite’s pathogenicity, host–pathogen interactions, environmental constraints and invasion biology. Comparative genomics and epigenomics analyses will provide deep understanding of parasitism biology for future diagnosis and prevention of trchinellosis. We provide a near-complete new T.p reference genome using SMRT technology, first time confirmed and characterized T.p DNA methylome, enabling full annotation. Based on this new version, we show repetitive sequences play important role in genome expansion, in synergy with DNA methylation during evolution. We further portrait the genomic and epigenomic regulation on E-S products in relation with their parasitism differences, especially for two super-families, including DNase II and EGF-like domain proteins.
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