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Relative abundance of the integrant-derived viral RNAs in infected tissues harvested from chronic HBV carriers

ABSTRACT: Relative abundance of the integrant-derived viral RNAs in infected tissues harvested from chronic HBV carriers

PROVIDER: PRJNA433507 | ENA |

REPOSITORIES: ENA

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Relative abundance of the integrant-derived viral RNAs in infected tissues harvested from chronic HBV carriers

Project description:Five matching sets of non-malignant liver tissues and HCCs from individuals chronically infected with hepatitis B virus (HBV) were examined. The HBV genomic sequences were determined using overlapping PCR amplicons covering the entire viral genome. Four pairs of tissues were infected with HBV of genotype C, while one pair - with genotype B. HBV replication markers were found in all tissues. In majority of HCC samples, the levels of pre-genomic/pre-core RNA (pgRNA) and covalently closed circular DNA (cccDNA) were lower than those of liver tissue counterparts. Regardless of the presence of HBV replication markers, (i) integrant-derived HBV RNAs (id-RNAs) were found using RT-PCR analysis in all tissues, and were considerably abundant or predominant in 6/10 tissue samples (2 livers and 4 HCCs); (ii) the RNAs that were polyadenylated using cryptic HBV polyadenylation signal and therefore could be produced by HBV replication or derived from integrated HBV DNA were found in 5/10 samples (3 livers and 2 HCCs), and were considerably abundant species in 3/10 tissues (2 livers and 1 HCC); and (iii) cccDNA-transcribed RNAs polyadenylated near position 1931 were not abundant in 7/10 tissues (2 livers and 5 HCCs), and were predominant only in two livers. Subsequent RNA sequencing analysis of selected liver/HCC samples also showed relative abundance of id-RNAs in most of examined tissues. Our findings suggesting that id-RNAs could represent a significant source of HBV envelope proteins, which is independent of viral replication, are discussed in the context of possible contribution of id-RNAs to the HBV life cycle.

2021-02-06 | GSE110345 | GEO

The transcriptional profiles of chronic HBV patients and asymptomatic carriers

Project description:The transcriptional profiles of chronic HBV patients and asymptomatic carriers

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Affymetrix SNP6.0 array data for different clinical outcomes of HBV infection

Project description:Chronic hepatitis B virus (HBV) infection is a serious global public health problem. To identify susceptibility loci for disease progression of HBV infection, we performed this genome-wide association study using DNA pools of case and control constructed by progressed HBV carriers (acute liver failure, liver cirrhosis, hepatocellular carcinoma) and asymptomatic HBV carriers separately. Performing GWAS on pools of DNA samples is an effective strategy to reduce the costs of studies and pooling DNA has been shown to be an efficient method to select candidate susceptibility loci for follow-up by individual genotyping. Affymetrix Genome-Wide Human Mapping SNP6.0 Arrays were performed for DNA pools, which were constructed by pooling 120 ng DNA from each participant. Four independent pools were created: case A was acute liver failure group (n = 86), case B was liver cirrhosis group (n = 88), case C was hepatocellular carcinoma group (n = 90) and case D was asymptomatic HBV carriers (n = 66) that was considered as control. Twelve chips (each pool was replicated in triplicate) were finished according to the manufacturer's instruction.

2013-12-10 | E-GEOD-26034 | biostudies-arrayexpress

Affymetrix SNP6.0 array data for different clinical outcomes of HBV infection

2013-12-10 | GSE26034 | GEO

Relative Abundance of Integrant-Derived Viral RNAs in Infected Tissues Harvested from Chronic Hepatitis B Virus Carriers.

Project description: Not available

| S-EPMC5923063 | biostudies-literature

The transcriptional profiles of chronic HBV patients and asymptomatic carriers

Project description:The study aims at investigating the specifical transcriptional signatures of chronic HBV patients

2021-02-16 | GSE166759 | GEO

Determination of the relative abundance of mRNAs in a polyribosome-associated pool

2011-07-21 | GSE26742 | GEO

RNASeq of total RNA isolated from self-assembling co-cultures of primary human hepatocytes (SACC-PHHs) mono-infected with HBV, co-infected with HBV/HDV, or uninfected at 8 and 28 days post-infection

Project description:Here, we examined the host response relative of SACC-PHHs infected with either hepatitis B virus (HBV) alone or both HBV/hepatitis delta virus (HDV) co-infection compared to non-infected controls.

2019-06-18 | GSE112118 | GEO

Comprehensive analysis of transcripts and proteins relative abundance during Plasmodium falciparum blood stages

Project description:Comprehensive analysis of transcripts and proteins relative abundance during Plasmodium falciparum blood stages

| PRJNA639823 | ENA

Determination of the relative abundance of mRNAs in a polyribosome-associated pool

Project description:Polyribosomal fractions derived from P25 mice were the starting material for IPs of the FMRP protein and associated mRNA. Therefore we wanted to determine the relative abundance of all mRNAs in the starting pool for the IP as a denominator with which to compare the IPed material. [mRNA profiling]: We prepared polyribosomes on sucrose gradients in duplicate from 2 FVB WT mice, age P25, and purified RNA from polyribosomal fractions of each of the two gradients.

2011-07-20 | E-GEOD-26742 | biostudies-arrayexpress

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