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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 16, 2024 |
| Title |
MCL-19020-2 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
agent: hepatitis B virus, replication in mouse
tissue: Liver
host foxa1_genotype: +/+
host foxa2_genotype: f/f
host foxa3_genotype: -/-
host albcre: -
host sex: F
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA were isolated from liver of HBV transgenic mice using the protocol as described by: Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162: 156–159. doi:10.1006/abio.1987.9999.
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).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
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| 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: HBV genome fasta file GSE242448_HBV.fa.gz from GSE242448
Supplementary files format and content: combined_methyl.txt: Tab-delimited text file of total coverage, methylated read coverage, and percent methylation for each sample.
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| Submission date |
Apr 02, 2024 |
| Last update date |
Jul 16, 2024 |
| Contact name |
Mark Maienschein-Cline |
| E-mail(s) |
mmaiensc@uic.edu
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| Organization name |
University of Illinois at Chicago
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| Department |
Research Resources Center
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| Lab |
Center for Research Informatics
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| Street address |
1819 W Polk Ave, Rm 336 M/C 789
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE263033 |
Foxa-deficiency Restricts Hepatitis B Virus Biosynthesis Through Epigenic Silencing [Bisulfite-Seq] |
| GSE263121 |
Foxa-deficiency Restricts Hepatitis B Virus Biosynthesis Through Epigenic Silencing |
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| Relations |
| BioSample |
SAMN40729972 |
| SRA |
SRX24135735 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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