Transcriptomics

Dataset Information

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RNA-seq of E. coli strains overproducing DNA "damage-up" proteins (DDPs)


ABSTRACT: This experiment assesses gene expression changes in response to the overproduction of DNA \"damage-up\" proteins (DDPs). These proteins, when overproduced, activate the SOS DNA damage response and were identified in a genome-wide overproduction screen using the mobile plasmid collection (Saka et al 2005). For the RNA-seq experiments, 7 DDP overproduction strains were compared to an empty vector control strain.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Escherichia coli K-12  

SUBMITTER: Devon M Fitzgerald   

PROVIDER: E-MTAB-7361 | ArrayExpress | 2019-01-15

SECONDARY ACCESSION(S): ERP111806

REPOSITORIES: ArrayExpress, ENA

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Publications

Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.

Xia Jun J   Chiu Li-Ya LY   Nehring Ralf B RB   Bravo Núñez María Angélica MA   Mei Qian Q   Perez Mercedes M   Zhai Yin Y   Fitzgerald Devon M DM   Pribis John P JP   Wang Yumeng Y   Hu Chenyue W CW   Powell Reid T RT   LaBonte Sandra A SA   Jalali Ali A   Matadamas Guzmán Meztli L ML   Lentzsch Alfred M AM   Szafran Adam T AT   Joshi Mohan C MC   Richters Megan M   Gibson Janet L JL   Frisch Ryan L RL   Hastings P J PJ   Bates David D   Queitsch Christine C   Hilsenbeck Susan G SG   Coarfa Cristian C   Hu James C JC   Siegele Deborah A DA   Scott Kenneth L KL   Liang Han H   Mancini Michael A MA   Herman Christophe C   Miller Kyle M KM   Rosenberg Susan M SM  

Cell 20190101 1-2


DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane  ...[more]

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