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Sample GSM3122306 Query DataSets for GSM3122306
Status Public on Feb 07, 2019
Title b880-H3-ChIP_2
Sample type SRA
 
Source name liver
Organisms Homo sapiens; Hepatitis B virus
Characteristics cell line: N/A
cell type: liver biopsy
tissue: liver
hbv genotype: C
disease stage: HBeAg+ hepatitis
ChIP: H3-ChIP
chip antibody: rabbit monoclonal B0422, abcam ab41969
Treatment protocol Biopsy specimens were thawed in pre-warmed 0.05% Trypsin-EDTA (ThermoFisher Scientific, Waltham, MA) and mixed with 8x106 uninfected HepG2-hNTCP cells.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in freshly prepared 1% formaldehyde in PBS (both ThermoFisher Scientific) for 5 min prior to quenching with 125 mM glycine in PBS. Pelleted cells were either used directly for analysis or snap-frozen and stored at -80°C until use. Next, cells were washed with cold lysis buffer [PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM dithiothreitol (DTT), 50 ng/ml trichostatin A (TSA) and 1x EDTA-free protease inhibitor (Roche, Basel, Switzerland)] and lysed in the same buffer for 10 min on ice. Nuclei were pelleted, resuspended in digestion buffer [H2O with 50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% glycerol, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)] and digested with 600 IU/ml micrococcal nuclease (MNase; ThermoFisher Scientific) for 12 min at 37°C. Digestion was stopped by addition of 10 mM EDTA. Nuclei were pelleted at 6500 x g and supernatants collected. The pellet was resuspended in digestion buffer with 10 mM EDTA and 300 mM NaCl and mildly sonicated using a W 375 sonicator (Qsonica, Newtown, CT) at 50% duty cycle and power setting 3. Nuclei were again pelleted, supernatants combined and mixed with an equal amount of sucrose buffer [H2O with 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM EDTA, 0.01% NP-40, 50 ng/ml TSA, and 1x EDTA-free protease inhibitor (Roche)]. Samples were concentrated using Amicon Ultra-4 100 kDa centrifugal filter units (Millipore-Sigma; Merck KGaA, Darmstadt, Germany) and spun on a 5-30% continuous sucrose gradient in sucrose buffer for 4 h at 40,000 x g and 4°C using a SW41Ti rotor (Beckman Coulter Inc., Brea, CA). Chemicals were obtained from Millipore-Sigma unless noted otherwise. Mononucleosome containing fractions were pooled and concentrated to ~500 µl prior to addition of 100 ng/µl bovine serum albumin (ThermoFisher Scientific). Mononucleosomes were either stored at -20°C or used immediately for ChIP. Antibodies were bound to 20 µl/ChIP Dynabeads Protein G (ThermoFisher) in ChIP buffer [H2O with 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 200 µg/ml BSA] at 4°C and added to 2 µg of chromatin in ChIP buffer and allowed to bind overnight. Samples were washed six times in LiCl wash buffer [H2O with 150 mM LiCl, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate] and eluted in 100 µl elution buffer [H2O with 1% SDS and 100 mM NaHCO3]. Crosslinks were reversed by digestion with Proteinase K (ThermoFisher) for 5 h at 65°C and then digested for another 30 min with DNase-free RNase A (ThermoFisher) at 37°C. DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
1 ng of DNA was used for sequencing library construction with the KAPA Hyper Prep Kit (Roche) according to the manufacturer’s instructions. For barcoding, 2 µl of TruSeq RNA adapters stocks were used (Illumina, Inc., San Diego, CA). Up to 6 libraries were pooled per sequencing run and 500 ng pooled library subject to HBV-specific target enrichment using the xGen Lockdown Reagents Hybridization and Wash Kit (Integrated DNA technologies, Skokie, IL) according to the manufacturer’s instructions. A custom set of xGen lockdown probes of 60 bp length tiling the entire HBV genome of genotypes A-D was used for target enrichment (Integrated DNA technologies) together with Dynabeads MyOne T-270 Streptavidin (ThermoFisher). The pull-down was amplified for 12 or 8 PCR cycles (biopsies vs. de novo infected cells/cell lines; KAPA HiFi HotStart ReadyMix, Roche) and the product cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Inc.). The product was used to dilute the original library to 20 nM. Sequencing was performed using an Illumina MiSeq sequencer with a MiSeq v3 reagent kit for 2x76 bp paired-end reads (Illumina, Inc.).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description run 2
Aligned to EU410079.1.
Data processing base calling: RTA 1.18.54 (from Illumina MCS 2.6.2)
alignment: bowtie2 2.3.0 was used for alignment to 1.1mer viral genomes (with -t -no-unal -no-discordant -no-mixed -I 120 -X 200 option) and all sequences (combined hg38/HBV/phiX; only -t option)
paired read merging: custom script was used to merge paired reads in the output SAM file based on viral genome coordinates. Unsequenced insert was represented as N with low quality score.
BAM conversion: SAM file was converted to BAM, sorted, and indexed using samtools 0.1.19
BEDGRAPH conversion: BAM file was converted to BEDGRAPH using bedtools 2.18.1 (-bg -trackline options)
1mer conversion: custom script was used to wrap around reads that aligned in the overhang of the 1.1mer to the start of the sequence
scaling and wig conversion: custom script was used to convert BEDGRAPH to WIG files while simultaneously scaling it per 106 total reads in the library (hg38+HBV+phiX)
Genome_build: HBV reference genomes are indicated in the sample overview (protocl column). GRCh38.p10 was used for the human genome, NC_001422.1 for phiX
Supplementary_files_format_and_content: WIG files contain the number of HBV reads per million total reads for each position of the respective HBV reference genome. Sequences are shifted by -500 nt compared to EcoRI site.
 
Submission date Apr 30, 2018
Last update date Feb 08, 2019
Contact name Tobias Flecken
E-mail(s) t.flecken@zoho.com
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
 
Platform ID GPL24950
Series (1)
GSE113879 Mapping the heterogeneity of histone modifications on hepatitis B virus-DNA using liver needle biopsies obtained from chronically infected patients
Relations
BioSample SAMN09004733
SRA SRX4014822

Supplementary file Size Download File type/resource
GSM3122306_b880-H3_2_hbvC_wrapped_scaled.wig.gz 1.3 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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