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Genome wide mapping of R-loops in the repriming deficient DT40 cells using DRIP-Seq

ABSTRACT: The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between chicken DT40 wild type and PrimPol knockout cells. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

ORGANISM(S): Gallus gallus Drosophila melanogaster

PROVIDER: GSE112746 | GEO | 2018/11/26

REPOSITORIES: GEO

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Repriming limits R-loop formation at DNA secondary structures during S phase

Project description:The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between wild type and PrimPol knockout cell lines. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

2018-11-26 | GSE112747 | GEO

Genome wide mapping of R-loops in the repriming deficient human cells using RNA DIP-Seq

Project description:The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between human wild type and PrimPol knockout human iPS cell lines. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

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Characterization of gene expression changes in IRF4-deficient DT40 B cells

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Expression data from chicken B cell lymphoma (DT40) cell lines.

Project description:Global gene expression profiling of the avian B-lymphoma DT40 cell line was used as a model to differentiate among Btk KO and Btk KO cells reconstituted with human Btk. Differences in the gene expression pattern showed statistically significant changes between parental DT40 and all the Btk KO cell populations irrespective of whether they are reconstituted or not. These results imply that in the process of generating a knockout cell line, subclones are selected, which have multiple changes in their gene expression pattern (p<0.01). Keywords: cell line

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Transcriptional Profiles in Bursal B-Lymphoid DT40 Cells Infected with Very Virulent Infectious Bursal Disease Virus

Project description:Infectious bursal disease virus (IBDV) causes a highly contagious, immunosuppressive disease in chickens. The virus mainly infects immature B lymphocytes in the bursa of Fabricius (BF). Chicken B cell line DT40, an avian leukosis virus-induced B cell line, supports very virulent IBDV (vvIBDV) infection in vitro and thereby serves as a good model for investigating the infection and pathogenesis of this virus. However, a transcriptome-wide understanding of the interaction between vvIBDV and B cells has not yet been achieved. This study aimed to employ time-course DNA microarrays to investigate gene expression patterns in DT40 cells after infection with vvIBDV strain LX.

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Evaluation of the chicken transcriptome by SAGE of B cell and the DT40 cell line

Project description:These libraries represent total RNA from bursal tissue of 20 day old CB-inbred chicks and the ALV induced bursal cell line DT40 Cre1 cells. Keywords = chicken transcriptome SAGE Bursal cell DT40 Keywords: other

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