Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Growth phase-coupled variation of mRNA levels. (A) E. coli W3110 was grown in LB. Cell growth was monitored by measuring the turbidity at 600 nm, and the number of viable cells was determined by measuring colonies on LB agar plates. (B and C) Microarray assays were carried out as described in Materials and Methods, first for mixtures of Cy3-labeled cDNAs for exponential-phase RNAs and Cy5-labeled cDNAs for stationary-phase RNAs and second with the opposite combination. The assays were repeated twice with independent cultures. The level of each mRNA at each point during the stationary phase, relative to the exponential-phase level, was calculated. For the mRNAs whose levels increased (B) or decreased (C) in the stationary phase, the culture time-dependent variation is shown for some representative species (for details see Tables ​Tables11 and ​and33).

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques: Microarray, Labeling

Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Genes up-regulated in the stationary phase in wild-type E. coli W3110 a

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques:

Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Genes down-regulated in the stationary phase in wild-type E. coli W3110 a

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques: Modification

Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Stationary-phase genes that were not activated in an RpoS sigma-defective mutant a

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques: Mutagenesis, Activity Assay

Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Promoters analyzed with the DFP vector

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques:

Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Growth phase-dependent variation of promoter activity. A total of 100 promoters, listed in Table ​Table4,4, were inserted into pGRP, and each of the resultant promoter assay plasmids was transformed into both wild-type E. coli KP7600 and its rpoS mutant JD22323. An overnight culture of each transformant grown in LB was transferred into fresh LB, and the culture was incubated at 37°C with shaking. The promoter activity was measured at nine times (0, 3, 4, 6, 8, 10, 12, 24, and 36 h). The activity of the test promoter relative to that of reference promoter lacUV5 was determined by determining the GFP/RFP ratio (for details see Materials and Methods). (A) RpoS-dependent promoters (group A); (B) RpoS-independent promoters (group B); (C) RpoS-independent promoters (group C); (D) weak promoters (group D).

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques: Activity Assay, Promoter Assay, Transformation Assay, Mutagenesis, Incubation

Journal:

Article Title: Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

doi: 10.1128/JB.186.21.7112-7122.2004

Figure Lengend Snippet: Promoters highly expressed in the stationary phase

Article Snippet: Mixtures of Cy3- and Cy5-labeled RNA were subjected to microarray analysis by using an E. coli DNA chip containing 4,028 DNA spots, each of which corresponded to one open reading frame (Takara version 1).

Techniques:

Journal:

Article Title: Comprehensive analysis of host gene expression in Autographa californica nucleopolyhedrovirus-infected Spodoptera frugiperda cells

doi: 10.1016/j.virol.2011.01.006

Figure Lengend Snippet: Patterns of host gene expression in AcMNPV-infected Sf21 cells determined by microarray analysis. Probes for host genes designed based on ESTs sequence data from SPODOBASE, http://bioweb.ensam.inra.fr/spodobase/). The approximate number of genes that were A) up-regulated or B) down-regulated during the time course of infection (6, 12, and 24 hpi) compared with the mock-infected controls; C) Chart comparing the expression trends exhibited by up- and down-regulated genes during the time course of infection. Only genes that their level of expression were equal to or more than 1.2 fold change and showed significant difference (p<0.05, ONE WAY ANOVA) were selected.

Article Snippet: Microarray Design A 44K Agilent oligonucleotide microarray chip was designed to include most of the known ESTs of Spodoptera frugiperda .

Techniques: Expressing, Infection, Microarray, Sequencing

Journal:

Article Title: Comprehensive analysis of host gene expression in Autographa californica nucleopolyhedrovirus-infected Spodoptera frugiperda cells

doi: 10.1016/j.virol.2011.01.006

Figure Lengend Snippet: Analysis of non-clathrin coat protein zeta 1-COP gene expression. Non-clathrin coat protein zeta 1-COP gene is represented by two different ESTs in SPODOBASE. A) SF9L03957-Contig1 (EST1) and Sf1P09405-5-1-Contig1 (EST2) that exhibit divergent expression patterns on microarrays. The fold change in expression for each probe, designated p1 - p6, at each time point is the average from four independent biological replicates. B) Diagram shows the relationship between EST1 and 2 and the locations of the microarray probes. Sequence comparisons reveal that both contigs share two common regions of nearly identical nucleotide sequence, indicated by the shaded black bars. The remaining sequences are unique to each EST, and depicted by either unfilled white or shaded grey bars. Probe 1 (p1) matches both contig sequences, p2-p3 are specific for the unique region of EST1, and p4 and p6 are specific for the unique region of EST2. Most of p5 is specific for the unique region of EST2, however it overlaps the small region of sequence identity shared with EST 1 (13 identical nucleotides).

Article Snippet: Microarray Design A 44K Agilent oligonucleotide microarray chip was designed to include most of the known ESTs of Spodoptera frugiperda .

Techniques: Expressing, Microarray, Sequencing

Journal:

Article Title: Comprehensive analysis of host gene expression in Autographa californica nucleopolyhedrovirus-infected Spodoptera frugiperda cells

doi: 10.1016/j.virol.2011.01.006

Figure Lengend Snippet: comparison between the average fold change of microarray and qRT-PCR

Article Snippet: Microarray Design A 44K Agilent oligonucleotide microarray chip was designed to include most of the known ESTs of Spodoptera frugiperda .

Techniques: Microarray

Journal: BMC Biotechnology

Article Title: Low density DNA microarray for detection of most frequent TP53 missense point mutations

doi: 10.1186/1472-6750-5-8

Figure Lengend Snippet: Detection of TP53 silent and missense base substitutions using DNA sequencing versus DNA microarray hybridization.

Article Snippet: In the present work we designed a novel small format DNA chip (genosensor array) to search for nine point mutations in codons 248, 249 and 273 of the TP53 gene.

Techniques: DNA Sequencing, Microarray, Hybridization, Sequencing, Mutagenesis

Journal: BMC Biotechnology

Article Title: Low density DNA microarray for detection of most frequent TP53 missense point mutations

doi: 10.1186/1472-6750-5-8

Figure Lengend Snippet: Layout of the TP53 low density DNA microarray . (A): Names and alignment of stacking oligonucleotides and probes to their respective synthetic wild type target sequence. Bold letters correspond to the nucleotide change in DNA sequence due to the point mutations. (B): Layout of the probe array on the glass slide. The probes were applied to the slide in triplicate as depicted at the top. The numbers correspond to the probes in Table 1.

Article Snippet: In the present work we designed a novel small format DNA chip (genosensor array) to search for nine point mutations in codons 248, 249 and 273 of the TP53 gene.

Techniques: Microarray, Sequencing