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Sample GSM7763648 Query DataSets for GSM7763648
Status Public on Nov 29, 2023
Title Control Male.4 [M14]
Sample type SRA
 
Source name Liver
Organism Hepatitis B virus
Characteristics tissue: Liver
genotype: HBV(+)Tet3(f/f)Cre(-)
Extracted molecule genomic DNA
Extraction protocol Bisulfite treatment of protein-free genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning Kit (D5030; Zymo Research, Inc., Irvine, CA, USA) according to the manufacturer's instructions. The three major viral amplicons covering 62 of the 99 CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite-treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument. Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps in a protocol termed targeted amplicon sequencing (TAS) The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’- TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (ii) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’ (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), and (iii) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina MiSeq
 
Description M14
HBV.fa
Data processing Raw paired-end sequence data were merged without trimming using the software package PEAR. Merged reads were mapped to the HBV reference DNA sequence (HBV.fa) using Bismark. Methylation status was called at each CpG using Bismark, and total counts, methylated counts, and percent methylation were computed for each CpG position.
Assembly: Custom (supplementary file HBV.fa)
Supplementary files format and content: methyl_levels.txt: Tab-delimited text file of total coverage, methylated read coverage, and percent methylation for each sample.
Supplementary files format and content: HBV.fa: fatsa file of hepatitis B virus sequence used as reference genome
 
Submission date Sep 06, 2023
Last update date Nov 29, 2023
Contact name Mark Maienschein-Cline
E-mail(s) mmaiensc@uic.edu
Organization name University of Illinois at Chicago
Department Research Resources Center
Lab Center for Research Informatics
Street address 1819 W Polk Ave, Rm 336 M/C 789
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
 
Platform ID GPL33735
Series (1)
GSE242448 Ten-eleven translocation (Tet) methylcytosine dioxygenases dependent viral DNA demethylation mediates in vivo hepatitis B virus (HBV) biosynthesis
Relations
BioSample SAMN37299370
SRA SRX21645784

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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