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Genome wide identification of BysR binding sites in Burkholderia sp. JP2-270

ABSTRACT: Genome wide identification of BysR binding sites in Burkholderia sp. JP2-270

PROVIDER: PRJNA798396 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17654700_1.fastq.gz	Fastqsanger.gz
	SRR17654700_2.fastq.gz	Fastqsanger.gz
	SRR17654698_1.fastq.gz	Fastqsanger.gz
	SRR17654698_2.fastq.gz	Fastqsanger.gz
	SRR17654699_1.fastq.gz	Fastqsanger.gz

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Genome wide identification of BysR binding sites in Burkholderia sp. JP2-270

Project description:To verify genes that are directly regulated by BysR, we used DNA affinity purification sequencing analysis (DAP-seq) for genome-wide recognition of BysR binding sites in vitro. The HALO-fusion BysR protein was successfully expressed and purified. After affinity purification and sequencing, at least 22 million double-end reads per sample were generated and with > 99 % of reads uniquely mapped to the JP2-270 genome. A total of 470 enriched common peaks of two replicates with –log10(P-value) ≥ 2 were called . The mean width of DAP-seq peaks was < 1,000. In total, 367 (78%) of these peaks were found to locate in the -1 kbp to 1 kbp regions by the analysis of peak summit positions relative to the start codons of JP2-270 open reading frames.

2022-11-22 | GSE193916 | GEO

Burkholderia sp. JP2-270

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Burkholderia sp. JP2-270

Project description:Burkholderia sp. JP2-270 Genome sequencing and assembly

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RNA-seq analysis of wild type and ΔbysR in Burkholderia sp. JP2-270

Project description:RNA-seq analysis of wild type and ΔbysR in Burkholderia sp. JP2-270

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Effect of recombinant IL-33s, particularly IL-3395-270, IL-3399-270,IL-33109-270, and IL-33112-270 in HRMVECs

Project description:To investigate the expression prolfile of genes regulated by IL-3395-270, IL-3399-270, IL-33109-270, and IL-33112-270 in HRMVECs.

2024-07-24 | GSE245784 | GEO

Transcriptome analysis of Aggregatibacter actinomycetemcomitans serotype b strains of JP2 and non-JP2 genotypes using a pan-genome microarray

2012-09-28 | GSE38943 | GEO

Transcriptome analysis of Aggregatibacter actinomycetemcomitans serotype b strains of JP2 and non-JP2 genotypes using a pan-genome microarray

Project description:To characterize the differences in pattern of gene expression between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Transcriptome analysis of 3 strains of JP2 and 2 strains of non-JP2 genotypes of A. actinomycetemcomitans was performed Transcripome of three strains of JP2 genotype (HK1651, D28S-1 and D41S-1) and two strains of non-JP2 genotype (SCC1398 and ANH9381) were examined where two biological duplicates were carried out for each strain.

2012-09-28 | E-GEOD-38943 | biostudies-arrayexpress

Comparative genomic analysis of Aggregatibacter actinomycetemcomitans of JP2 and non-JP2 genotypes using a pan-genome microarray

2012-09-28 | GSE39143 | GEO

RNA-seq analysis of wild type and ΔbysR in Burkholderia sp. JP2-270

Project description:Purpose: In order to identify the differentially expressed genes between wild type and ΔbysR, we performed RNA-seq analysis.Methods：All the isolates were cultured in CM medium for 24 h at 28℃. Three repetitions were performed for each treatment. The samples were sequenced on an Illumina Hiseq 2000 platform.Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Results：A total of 9-13 million clean reads were obtained per replicate, each read with an average length of 150 bp. The square (R2) of Pearson correlation coefficient is greater than 0.903 between samples (supplementary Fig. S1) indicated that the data had a good reproducibility. Differential expression analysis of samples from WT and ΔbysR was performed, and revealed 350 differentially expressed genes (DEGs) consisting of up-regulated (302) and down-regulated genes (48) (with p-adj<0.05, |log2(FoldChange)|> 1) in ΔbysR compared to the WT.

2022-11-22 | GSE193778 | GEO

Comparative genomic analysis of Aggregatibacter actinomycetemcomitans of JP2 and non-JP2 genotypes using a pan-genome microarray

Project description:To assess the performance of our custom-designed pan-genome microarray and characterize the differences in gene content between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Comparative genomic hybridization reactions were carried out to assess the performance of our pan-genome microarray by using genomic DNA of 11 previously sequenced Aggregatibacter actinomycetemcomitans strains (I23C, SCC1398, ANH9381, HK1651, D7S-1, D11S-1, I63B, SCC393, D18P-1, SCC2302, and D17P-2). The microarray was subsequently used for comparative genomic hybridization of 6 strains of JP2 (S067, A26, G111-1, G121-2, D41S-1, and HK1651) and 6 strains non-JP2 (I23C, SCC1398, ANH9381, ATCC29524, 194, and G104-2) genotypes of Aggregatibacter actinomycetemcomitans. Two biological duplicates were carried out for each strain.

2012-09-28 | E-GEOD-39143 | biostudies-arrayexpress

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