Geobacillus zalihae NBRC 101842
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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:Geobacillus kaustophilus NBRC 102445 strain:ATCC 8005 Genome sequencing
| PRJNA531185 | ENA
Project description:Geobacillus stearothermophilus T6 genome sequencing project
| PRJNA38101 | ENA
Project description:Geobacillus stearothermophilus t1 genome sequencing project
| PRJNA38099 | ENA
Project description:To investigate the transcriptional profile of GVE2 genes, the viral genes were identified by DNA microarray with Cy5- or Cy3-dUTP-labeled cDNAs prepared from uninfected and GVE2-infected Geobacillus sp. E263 at 4 h p.i.. After hybridization with the Cy3-dUTP-labeled cDNAs from GVE2-infected Geobacillus sp. E263 at 4 h p.i., Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263 as well as Cy3- dUTP-labeled yeast cDNAs and Hex DNA, many spots produced positive signals significantly above the background, while no signal appeared for the Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263., indicating that the positive signals represented the GVE2 gene transcripts detectable by DNA microarray. The DNA fragments, detected to be positive in the reverse transcripts at 4 h p.i., contained 74.2% of the presumptive GVE2 ORFs. Keywords: Transcriptional profile of thermophilic bacteriophage at 4 h p.i. A DNA microarray containing 82 DNA fragments of the viral genome was constructed following a PCR-based microarray method. Briefly, specific primer sets were designed to amplify approximately 500-bp fragment each using viral genome as template. All PCR products showing a single band of the appropriate size by gel electrophoresis were purified, and reconstituted in TE buffer at a final concentration of about 500 μg/ml for spotting in triplicates onto the silylated-glass slides (CEL Associates, Inc. USA) using a microarrayer (Smart Arrayer 48, CapitalBio). Eight DNA fragments from yeast genome and a randomly synthesized DNA fragment (Hex) were included as exogenous positive controls to normalize the microarry date. Distilled water was used as negative controls. Total RNAs were isolated from the uninfected and phage-infected Geobacillus sp. E263 cells at 4 h postinfection. The cDNAs from uninfected Geobacillus sp. E263 were labeled with Cy5 and the cDNAs from phage-infected Geobacillus sp. E263 labeled with Cy3. At the same time, the cDNAs from yeast and the Hex DNA were labeled with Cy3. The Cy5- or Cy3-dUTP-labeled cDNAs were resuspended in hybridization solution and hybridized with the microarrays for 16 to 18 h at 42°C. Then the microarrays were rinsed several times following the standard method. Following the washing steps, the microarrays were dried by low-speed centrifugation (500 g for 5 min), and immediately scanned using a GenePix 4000B array scanner (Axon Instruments, Inc.). Images obtained from scanning were analyzed by GenePix Pro 4.0 array analysis software (Axon Instruments, Inc.)
2010-06-10 | E-GEOD-5577 | biostudies-arrayexpress