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ABSTRACT:
PROVIDER: PRJNA1294229 | ENA |
REPOSITORIES: ENA
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Project description:Purpose:The goals of this study are to clarify the B. subtilis NBRC 16449 response to soybeans. Methods: B. subtilis NBRC 16449 cells were aerobically cultured in liquid LB, LB solidified with agar, or on surface of boiled soybeans to logarithmic growth phase. Total RNAs were extracted from bacterial cells by Hot-Phenol method. Samples for RNA-seq were prepared according to Illmina protocol available from the manufacture. The sequence reads that passed quality filters were analyzed at the transcript isoform level with bowtie v0.11.2. Results: Using an optimized data analysis workflow, we mapped around 15 million sequence reads per sample to the whole genome of B. subtilis BEST195 and identified 4271 transcripts in B. subtilis NBRC 16449 with Bowtie aligner. Read count per genome was extracted from known gene annotations with HTSeq program. Compared the transcriptomes of B. subtilis NBRC 16449 grown on LB solidified with agar to that grown on surface of boiled soybeans, about 5% of genes showed the different expression levels.
2020-11-02 | GSE109523 | GEO
Project description:Whole-genome resequencing of eight transcription factor mutants and one wild-type, in order to verify the T-DNA insertion site and its uniqueness.
2017-08-15 | GSE102126 | GEO
Project description:Copy Number Variations (CNVs) were identified performing Comparative Genomic Hybridization (CGH) on 225 patients after whole-genome amplification, using Agilent SurePrint G3 4x180K microarrays. CNVs were further integrated with gene expression (Affymetrix U133+2 arrays) and mutations (targeted DNA resequencing). Complete description of the methods, array quality checks and called segments are available as supplemental material in the corresponding publication.
2019-10-24 | GSE136962 | GEO
Project description:Background: Evolutionary engineering is a powerful approach to isolate suppressor mutants and industrially relevant genotypes. Until recently, DNA microarray analysis was the only affordable genome-wide approach to identify the responsible mutations. This situation has changed due to the rapidly decreasing costs of whole genome (re)sequencing. DNA microarray-based mRNA expression analysis and whole genome resequencing were combined in a study on lactate transport in Saccharomyces cerevisiae. Jen1p is the only S. cerevisiae lactate transporter reported in literature. To identify alternative lactate transporters, a jen1Δ strain was evolved for growth on lactate. Results: Two independent evolution experiments yielded Jen1p-independent growth on lactate (μmax 0.14 and 0.18 h-1 for single-cell lines IMW004 and IMW005, respectively). Whereas mRNA expression analysis did not provide leads, whole-genome resequencing showed different single nucleotide changes (C755G/Leu219Val and C655G/Ala252Gly) in the acetate transporter gene ADY2. Analysis of mRNA levels and depth of coverage of DNA sequencing combined with karyotyping, gene deletions and diagnostic PCR showed that in IMW004 an isochromosome III (~475 kb), which contains two additional copies of ADY2C755G, was formed via crossover between YCLWΔ15 and YCRCΔ6. Introduction of the ADY2 alleles in a jen1 ady2 strain resulted in growth on lactate (μmax 0.14 h-1 for Ady2pLeu219Val and 0.12 h-1 for Ady2pAla252Gly). Conclusions: Whole-genome resequencing of yeast strains obtained from independent evolution experiments enabled rapid identification of a key gene that was not identified by mRNA expression analysis of the same strains. Reverse metabolic engineering showed that mutated alleles of ADY2 (C655G and C755G) encode efficient lactate transporters.
2011-12-21 | GSE31634 | GEO
Project description:Illumina human Omni5Exome arrays were used to investigate CNVs in Sѐzary syndrome tumours as part of a larger study involving whole exome sequencing of the same samples and targeted resequencing of a further cohort.
2016-07-22 | GSE80650 | GEO
Project description:Four groups of C57 mice were gavaged with CMC, ethanol, DEHP and ethanol+DEHP for 28 continuous days. At the end of the experiment, livers were harvested to carry out Whole genome resequencing, we found that metabolism related genes were significantly changed in the DEHP and ethanol+DEHP groups compared with control groups, but there was no significant change between them.
2019-01-01 | GSE121057 | GEO
Project description:Purpose: The goals of this study are to identify what gene GmRAV1 was related to. RNA-Sequencing experiments were designed between GmRAV1-ox soybeans and DN50 soybeans. Methods: Leaves mRNA of 30-day-old DN50 and GmRAV1-ox soybeans were used by RNA sequencing using Illumina HiSeqTM2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Genome_build: Glycine max Wm82.a2.v1 Results: RNA-seq data confirmed that there are 1467 genes with significant differences. Some genes expression of cytokinin and auxin signaling pathways is dramatically changed, such as GmARR9, GmAUX22, GmPIN1, GmCycD3 and GmPDV2. Conclusions: GmRAV1 are related to cytokinin and auxin signaling pathways.
2018-12-30 | GSE103490 | GEO