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    ATCC genome assemblies
    Genome Assemblies, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    refseq assembly genome sequences gcf 903797665 1  (ATCC)


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    ATCC refseq assembly genome sequences gcf 903797665 1
    Refseq Assembly Genome Sequences Gcf 903797665 1, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    genome assemblies  (ATCC)


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    ATCC genome assemblies
    Genome Assemblies, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    genome assemblies  (ATCC)


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    ATCC genome assemblies
    Genome Assemblies, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    genome assemblies  (ATCC)


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    ATCC genome assemblies
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    genome assemblies  (ATCC)


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    ATCC genome assemblies
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    a baumannii genome assembly  (ATCC)


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    ATCC a baumannii genome assembly
    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. <t>baumannii</t> 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.
    A Baumannii Genome Assembly, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978"

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    Journal: Frontiers in Cellular and Infection Microbiology

    doi: 10.3389/fcimb.2023.1324091

    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.
    Figure Legend Snippet: Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.

    Techniques Used: Mutagenesis, Expressing

    Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.
    Figure Legend Snippet: Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.

    Techniques Used: Expressing, Mutagenesis

    Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.
    Figure Legend Snippet: Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Techniques Used: Mutagenesis

    Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.
    Figure Legend Snippet: Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.

    Techniques Used: Expressing

    Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).
    Figure Legend Snippet: Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).

    Techniques Used: Expressing

    17978 genome assembly  (ATCC)


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    ATCC 17978 genome assembly
    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and <t>(C)</t> <t>umuDAb</t> mutant strains of A. baumannii <t>17978</t> JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.
    17978 Genome Assembly, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/17978 genome assembly/product/ATCC
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    1) Product Images from "DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978"

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    Journal: Frontiers in Cellular and Infection Microbiology

    doi: 10.3389/fcimb.2023.1324091

    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.
    Figure Legend Snippet: Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.

    Techniques Used: Mutagenesis, Expressing

    Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.
    Figure Legend Snippet: Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.

    Techniques Used: Expressing, Mutagenesis

    Genes repressed after DNA damage that are regulated by ddrR or  umuDAb  .
    Figure Legend Snippet: Genes repressed after DNA damage that are regulated by ddrR or umuDAb .

    Techniques Used:

    Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.
    Figure Legend Snippet: Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Techniques Used: Mutagenesis

    Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.
    Figure Legend Snippet: Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.

    Techniques Used: Expressing

    Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).
    Figure Legend Snippet: Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).

    Techniques Used: Expressing

    17978 genome assembly  (ATCC)


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    ATCC 17978 genome assembly
    Genes repressed after DNA damage that are regulated by ddrR or umuDAb .
    17978 Genome Assembly, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/17978 genome assembly/product/ATCC
    Average 86 stars, based on 1 article reviews
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    1) Product Images from "DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978"

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    Journal: Frontiers in Cellular and Infection Microbiology

    doi: 10.3389/fcimb.2023.1324091

    Genes repressed after DNA damage that are regulated by ddrR or umuDAb .
    Figure Legend Snippet: Genes repressed after DNA damage that are regulated by ddrR or umuDAb .

    Techniques Used:

    Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.
    Figure Legend Snippet: Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Techniques Used: Mutagenesis

    genome assemblies  (ATCC)


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    ATCC genome assemblies
    Genome Assemblies, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genome assemblies/product/ATCC
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    ATCC genome assemblies
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    ATCC refseq assembly genome sequences gcf 903797665 1
    Refseq Assembly Genome Sequences Gcf 903797665 1, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC a baumannii genome assembly
    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. <t>baumannii</t> 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.
    A Baumannii Genome Assembly, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/a baumannii genome assembly/product/ATCC
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    ATCC 17978 genome assembly
    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and <t>(C)</t> <t>umuDAb</t> mutant strains of A. baumannii <t>17978</t> JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.
    17978 Genome Assembly, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/17978 genome assembly/product/ATCC
    Average 86 stars, based on 1 article reviews
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    17978 genome assembly - by Bioz Stars, 2024-03
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    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.

    Article Snippet: The first widely used A. baumannii genome assembly and annotation (ATCC 17978) had all pAB3 genes combined with the chromosome.

    Techniques: Mutagenesis, Expressing

    Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.

    Article Snippet: The first widely used A. baumannii genome assembly and annotation (ATCC 17978) had all pAB3 genes combined with the chromosome.

    Techniques: Expressing, Mutagenesis

    Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Article Snippet: The first widely used A. baumannii genome assembly and annotation (ATCC 17978) had all pAB3 genes combined with the chromosome.

    Techniques: Mutagenesis

    Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.

    Article Snippet: The first widely used A. baumannii genome assembly and annotation (ATCC 17978) had all pAB3 genes combined with the chromosome.

    Techniques: Expressing

    Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).

    Article Snippet: The first widely used A. baumannii genome assembly and annotation (ATCC 17978) had all pAB3 genes combined with the chromosome.

    Techniques: Expressing

    Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Global transcriptomic analysis of differentially expressed genes after MMC treatment for (A) wildtype (WT), (B) ddrR , and (C) umuDAb mutant strains of A. baumannii 17978 JH. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the greatest induction or repression are labelled.

    Article Snippet: Notably, we newly identified eight genes as being regulated by ddrR or umuDAb , five of which were not annotated in the ATCC 17978 genome assembly ( ).

    Techniques: Mutagenesis, Expressing

    Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Venn diagram of differential gene expression, showing genes that were (A) repressed or (B) induced after MMC treatment (q < 0.05 for each) in wildtype (WT), ddrR , and umuDAb mutant strains of A. baumannii 17978 JH.

    Article Snippet: Notably, we newly identified eight genes as being regulated by ddrR or umuDAb , five of which were not annotated in the ATCC 17978 genome assembly ( ).

    Techniques: Expressing, Mutagenesis

    Genes repressed after DNA damage that are regulated by ddrR or  umuDAb  .

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Genes repressed after DNA damage that are regulated by ddrR or umuDAb .

    Article Snippet: Notably, we newly identified eight genes as being regulated by ddrR or umuDAb , five of which were not annotated in the ATCC 17978 genome assembly ( ).

    Techniques:

    Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Genes responsive to MMC treatment in WT, ddrR and umuDAb mutant strains. RNASeq data of log 2 fold changes is shown and categorized by response to MMC treatment, either repressed after treatment (panels A and B) or induced after treatment (panel C). (A) Genes that were repressed in the WT strain and whose repression was regulated by both ddrR and umuDAb (DR, UD), neither gene (-), or umuDAb (UD). (B) Genes that were not repressed in the WT strain but were repressed in the ddrR and/or umuDAb mutant strains. (C) Genes newly identified as induced after MMC treatment in this study. Shown are all eight induced genes regulated by either ddrR or umuDAb , or both genes, or neither gene (-). Unregulated genes include chromosomal gene KZA74_00195 and several CP genes (KZA74_12740 and 12885 from CP5, 07595 and 07650 from CP9, and 10340 and 10460 from CP14). Asterisks denote genes that had not been previously annotated in A. baumannii ATCC 17978. Numbers for gene names represent the KZA74 gene annotations.

    Article Snippet: Notably, we newly identified eight genes as being regulated by ddrR or umuDAb , five of which were not annotated in the ATCC 17978 genome assembly ( ).

    Techniques: Mutagenesis

    Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Global transcriptomic analysis of genes that were differentially expressed in WT A. baumannii 17978 JH cells vs mutants in (A) ddrR , (B) umuDAb , or (C) recA . Only untreated cells’ RNASeq data was combined and used in this analysis. Volcano plots show the log2 fold changes in gene expression where each dot represents one gene. Red and pink dots indicate significance at the q < 0.01 or q < 0.05 level. The log2 fold change is plotted on the x-axis, and the y-axis shows the log10 of the p value. The 10 genes with the highest induction or expression are labelled.

    Article Snippet: Notably, we newly identified eight genes as being regulated by ddrR or umuDAb , five of which were not annotated in the ATCC 17978 genome assembly ( ).

    Techniques: Expressing

    Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

    doi: 10.3389/fcimb.2023.1324091

    Figure Lengend Snippet: Venn diagram of differential gene expression, showing genes whose basal expression was (A) upregulated or (B) downregulated in WT A. baumannii 17978 JH cells vs ddrR and umuDAb mutants (q < 0.05 for each).

    Article Snippet: Notably, we newly identified eight genes as being regulated by ddrR or umuDAb , five of which were not annotated in the ATCC 17978 genome assembly ( ).

    Techniques: Expressing