Guangxi soil
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1253391 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Liver tissues of Guangxi Ma chicken from 32-week old with m performance, 50-week old with high and low laying performance, and 72-week old with high and low laying performance were collected and sequenced in quadruplicate using RNA-seq. The sequences were double-ended sequenced on the DNBSEQ sequencing platform. The sequence reads were quality controlled and then aligned with genomic sequences using HISAT2 program, quantified by featureCounts program, and gene expression levels were verified by qRT-PCR with SYBR Green detection. The results will be helpful to explore the factors that affecting laying performance from the perspective of yolk synthesis and provide a theoretical basis for improving the egg production of Guangxi Ma chicken.
2022-10-08 | GSE193655 | GEO
Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
2020-01-14 | GSE143587 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
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Project description:We report raw bulk RNA sequencing data rice roots (X.kitaake) protoplasted for 2.5 hours and 3 hours to eliminate the effects of protoplasting duration on our scRNA-seq analysis, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions to verify our findsing with scRNA-seq studies
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Project description:We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress
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Project description:More and more studies have shown that mRNAs and non-coding RNAs are involved in human diseases and various biological processes of animals, and play an important functional role in animal muscle growth and development. In this study, the expression levels of myogenic marker molecules MYOD1, MYOG, and MyHC increased after cattle muscle stem cells transition from proliferation to differentiation, which promoted the differentiation and maturation of cells. Then, we used RNA sequencing and bioinformatics to analyze the RNA expression of muscle stem cell proliferation phase (GM) and differentiation phase (DM). The results showed that 19,341 protein-coding RNAs (mRNAs) and 12,920 non-coding RNAs participated in the proliferation and differentiation of cattle muscle stem cells. And there were 2,148 differential mRNAs and 888 non-coding RNAs, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. These differentially expressed mRNAs are enriched in ECM receptor function, cell cycle, TGF-beta, PI3K-Akt and other signaling pathways, covering biological processes such as cell proliferation, invasion, differentiation, and autophagy. At the same time, we verified the expression levels of 7 mRNAs, 3 miRNAs, 2 lncRNAs, and 12 circRNAs by real-time quantitative PCR analysis, and selected circUBE2Q2 for functional verification. The expression profiling analysis showed that circUBE2Q2 was expressed in multiple tissues, and its expression in muscle stem cell differentiation phase was significantly higher than that in proliferation phase. In vitro cell experiments, circUBE2Q2 significantly promoted the differentiation and apoptosis of MuSCs and had no effect on proliferation. It indicates that circRNA plays a role in the muscle development of Guangxi cattle. Our research revealed the role of RNA expression in the proliferation and differentiation of Guangxi cattle muscle stem cells. These results provide new clues for the analysis of the mechanism by which mRNAs and non-coding RNAs regulate the proliferation and differentiation of Guangxi cattle muscle stem cells.
2021-06-12 | GSE152398 | GEO
Project description:Burkholderia pseudomallei can adapt to and thrive in a variety of environments, including soil and water, and also can infect different hosts, including humans, leading to the tropical disease melioidosis. Modulation of gene and protein expression is one of this pathogen's adaptive survival mechanisms, which could lead to changes in the bacteria's cell membrane, metabolism, and virulence. To better understand bacterial adaptation and host-pathogen interactions, this study compared the expression profiles of B. pseudomallei from infected mice to B. pseudomallei cultivated in soil extract media. B. pseudomallei in vivo was created by infecting mice through the intraperitoneal route and harvesting the spleens on day 5 post infection. Total RNA was isolated and sequenced from the harvested spleen. Sequence reads were mapped to the B. pseudomallei UKMD286 strain genome sequence.
2022-07-22 | E-MTAB-11200 | biostudies-arrayexpress
Project description:Eocanthecona furcellata isolate:Guangxi Hechi Genome sequencing
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Project description:Evaluation of different strategies to interpret metaproteomics data acquired on soil samples from a floodplain along the Seine River (France) incorporating sample-specific metagenomics data, soil genome catalogue database, and generic sequence database.
2022-02-17 | PXD026798 | Pride
Project description:Sex condition has been demonstrated to alter meat quality and sex is a major factor that affects the fatty acid composition of lipids of carcass dissectible or intramuscular depot fats. But the possible genetic molecular mechanism of gender causing meat quality differences is not well defined. Qinchuan cattle, Qinghai yak and Guangxi buffalo are three typical indigenous species of cattle in China. Obivious differences of meat quality exist among the three species of cattle. Few studies have been conducted to elucidate the muscle tissue expression of genes involved in pathways and mechanisms leading to meat quality differences beyond the phenotype properties of beef. Bovine Genome Arrays were used to construct muscle expression profiles of the longuissimus dorsi from Qinchuan cattle at 36 months and screen differentially expressed genes in the longuissimus dorsi muscle tissues among different genders of Qinchuan cattle, between Qinchuan cattle and Qinghai yak, and between Qinchuan cattle and Guangxi buffalo.
2009-12-23 | GSE19586 | GEO