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Series GSE123715 Query DataSets for GSE123715
Status Public on Dec 31, 2021
Title Binding of Nucleolin to HBV cccDNA
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Covalently closed circular DNA (cccDNA) forms the basis for replication and persistence of hepatitis B virus (HBV) in the chronically infected liver. In this study we sought to identify host factors interacting with the HBV genome. Nucleolin (Ncl) was identified as a potential interactor of HBV cccDNA. This interaction was veriefied using an established ChIPseq protocol. The data show that Ncl binds cccDNA albeit at lower levels than HBcAg. Ncl deposition occurs across the genome without a clear localization and a variable pattern of deposition between experiments. This verifies the interaction of Ncl with HBV-cccDNA.
Overall design 6 biological replicates of HepG2-hNTCP cell lines were infected with cell culture-derived HBV and used for ChIPseq using antibodies against Ncl, HBcAg, and H3K4me3 as control. Replicates HBV1-3 were processed directly after fixation, HBV4-6 were snap-frozen at -80°C after fixation prior to chromatin isolation. After ChIP, DNA was purified and used for library preparation. Pooled libraries were subject to HBV-specific target enrichment and the product combined with the original library pool. Sequencing was performed using an Illumina MiSeq.
Contributor(s) Xia Y, Flecken T, Skewes-Cox P, Holdorf MM, Liang TJ
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Submission date Dec 12, 2018
Last update date Jan 01, 2022
Contact name Tobias Flecken
Organization name Novartis Institutes for Biomedical Research
Department Infectious Diseases
Street address 5300 Chiron Way
City Emeryville
State/province CA
ZIP/Postal code 94608
Country USA
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (20)
GSM3510071 HBV1-input
GSM3510072 HBV1-HBcAg
GSM3510073 HBV1-Ncl
BioProject PRJNA509631
SRA SRP173331

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Supplementary file Size Download File type/resource
GSE123715_RAW.tar 60.0 Kb (http)(custom) TAR (of WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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