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Series GSE55699 Query DataSets for GSE55699
Status Public on May 18, 2015
Title Host genomic regions susceptible to damage during H. pylori infection
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We identify here host genomic regions that are more likely to be damaged during an infection with the human gastirc pathogen Helicobacter pylori and characterize underlying features of them. By ChIP-seq we obtained global information about the localization of the DNA-damage marker H2AXpS139. We used 20 ng of immunoprecipitated DNA of the human gastric cell line AGS to produce 240 mio sequence reads in total and compared the damage-pattern of 6 h and 19 h infected cells with that of 10 Gy irradiated ones. While the overall levesl of DNA damage wetre similar in terms of broken DNA and accumulation of H2AXpS139, infection-induced damage clearly accumulates towards the ends of chromosomal arms, namely telomere-proximal and close to centromeres, it also enriches mainly in genic and especially in transcribed regions. We show, taht this damage pattern is unique to the infection, occurs also in human non-transformed gastric epithelial cells and shows some correlation with previously identified cancer-related genes.
Overall design Examination of a DNA-damage induced histone modification from four different conditions.
Contributor(s) Meyer TF, Koeppel M
Citation(s) 26074077
Submission date Mar 07, 2014
Last update date May 15, 2019
Contact name Thomas F Meyer
Phone 03028 460 404
Organization name Max Planck Institute for Infection Biology
Department Molecular Biology
Street address Chariteplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1341955 H2AXpS139-ChIP-seq non-infected rep1
GSM1341956 H2AXpS139-ChIP-seq non-infected rep2
GSM1341957 H2AXpS139-ChIP-seq 6 h H.pylori rep1
BioProject PRJNA240573
SRA SRP039552

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Supplementary file Size Download File type/resource
GSE55699_RAW.tar 280.0 Kb (http)(custom) TAR (of TXT)
GSE55699_RNA_seq_gene_exp.diff.gz 1.5 Mb (ftp)(http) DIFF
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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