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SRX24135732: GSM8184232: MCL-19017-1; Mus musculus; Bisulfite-Seq
3 ILLUMINA (Illumina MiSeq) runs: 114,591 spots, 69M bases, 37.3Mb downloads

External Id: GSM8184232_r1
Submitted by: Center for Research Informatics, Research Resources Center, University of Illinois at Chicago
Study: Foxa-deficiency Restricts Hepatitis B Virus Biosynthesis Through Epigenic Silencing [Bisulfite-Seq]
show Abstracthide Abstract
In the HBV transgenic mouse model of chronic infection, the forkhead box protein A/hepatocyte nuclear factor 3 (Foxa/HNF3) family of pioneer transcription factors are required to support postnatal viral demethylation and subsequent HBV transcription and replication. Liver-specific Foxa-deficient mice with hepatic expression of only Foxa3 do not support HBV replication but display biliary epithelial hyperplasia with bridging fibrosis. However, liver-specific Foxa-deficient mice with hepatic expression of only Foxa1 or Foxa2 also successfully restrict viral transcription and replication but display only minimal alterations in liver physiology. These observations suggest that the level of Foxa activity, rather than the combination of specific Foxa genes, is a key determinant of HBV biosynthesis. Together, these findings suggest that targeting Foxa activity could lead to HBV DNA methylation and transcriptional inactivation, resulting in the resolution of chronic HBV infections which are responsible for approximately one million deaths annually worldwide. Overall design: Protein-free HBV transgenic mouse DNA from liver was subjected to bisulfite treatment, PCR amplification and sequencing to determine HBV DNA methylation status.
Sample: MCL-19017-1
SAMN40729975 • SRS20920357 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM8184232
Instrument: Illumina MiSeq
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Construction 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).
Runs: 3 runs, 114,591 spots, 69M bases, 37.3Mb
Run# of Spots# of BasesSizePublished
SRR2853536039,06123.5M12.7Mb2024-07-16
SRR2853536132,17819.4M9.6Mb2024-07-16
SRR2853536243,35226.1M14.9Mb2024-07-16

ID:
32446459

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