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

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

PROVIDER: PRJNA797844 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17638176_1.fastq.gz	Fastqsanger.gz
	SRR17638176_2.fastq.gz	Fastqsanger.gz
	SRR17638177_1.fastq.gz	Fastqsanger.gz
	SRR17638177_2.fastq.gz	Fastqsanger.gz
	SRR17638178_1.fastq.gz	Fastqsanger.gz

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Burkholderia sp. JP2-270

Project description:Burkholderia sp. JP2-270 Raw sequence reads

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Burkholderia sp. JP2-270

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

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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

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

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

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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.

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Expression analysis, A. actinomycetemcomitans wild type (JP2) vs CRP deletion mutant both grown anaerobically.

2011-06-01 | GSE25459 | GEO

Expression analysis, A. actinomycetemcomitans wild type (JP2) vs CRP deletion mutant both grown anaerobically.

Project description:The goal of this analysis is to define the anaerobic regulon for the global transcription factor CRP (catabolite repressor protein) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the CRP gene. Both strains were grown anaerobically. A three biological replicates study using total RNA recovered from three separate cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and three separate cultures of strain AAM167, an isogenic deletion mutant in which the gene for cAMP-Receptor-Protein (CRP) has been replaced by a spectinomycin resistance gene cassette. The cells were grown anaerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651. There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array. Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array. Wild type and mutant RNAs from cultures #1 and #2 were hybridized to the same chip and the RNAs from cultures #3 were hybridized in different quadrants of a second chip.

2011-06-01 | E-GEOD-25459 | biostudies-arrayexpress

Expression analysis of A. actinomycetemcomitans wild type (JP2) vs. Mlc deletion mutant both grown aerobically and anaerobically

Project description:The goal of this analysis is to define the aerobic and anaerobic regulons for the transcription factor Mlc (Makes Large Colonies) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the Mlc gene. Both strains were grown aerobically and anaerobically. The results show that Mlc is involved in the regulation of dozens of genes in both growth conditions. Half of the study (anaerobic samples) was a four biological replicates study using total RNA recovered from four separate anaerobic cultures of wild-type Aggregatibacter (formerly Actinobacillus) actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant in which the gene for Mlc (Makes Large Colonies) has been replaced by a spectinomycin resistance gene cassette. The cells were grown anaerobically in pairs (wild type paired with mutant). The second half of the study (aerobic samples) was a four biological replicates study using total RNA recovered from four separate aerobic cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant of Mlc. The cells were grown aerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651. There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array. Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array. A total of four chips were used in these experiments.

2013-06-01 | E-GEOD-38868 | biostudies-arrayexpress

Expression analysis of A. actinomycetemcomitans wild type (JP2) vs. Mlc deletion mutant both grown aerobically and anaerobically

2013-06-01 | GSE38868 | GEO

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.

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