Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA171394 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR526898.fastq.gz | Fastqsanger.gz | |||
| SRR526898_1.fastq.gz | Fastqsanger.gz | |||
| SRR526898_2.fastq.gz | Fastqsanger.gz | |||
| SRR526899.fastq.gz | Fastqsanger.gz | |||
| SRR526899_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
Project description:XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain is derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection.
2012-09-01 | GSE39684 | GEO
Project description:XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain is derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection. The Virochip microarray (version 5.0, Viro5AGL-60K platform) was used to screen RNA extracts from prostate tissue for XMRV to determine whether there is an association between the virus and prostate cancer. We used the ViroChip microarray to screen 22 archived prostate biopsies extracted in 2006 and 39 prospectively collected prostate biopsies for the virus, Xenotropic Murine Leukemia Virus-Related Virus (XMRV). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes [PMID 21779173], including all of the viral probes from the previous v2.0 (MV), v3.0 (V3) and v4.0 (V4) designs [PMIDs 18768820, 16983602, 16609730, 12429852, 9843981]. For this study, 61 experimental ViroChip microarrays derived from prospectively collected RNA extracted prostate tissue and frozen RNA from archived prostate from a 2006 study were analyzed. Additionally, two XMRV-positive control microarrays from the cell line, 22Rv1, were hybridized, for a total of 63 ViroChip microarrays. Some RNA extracts were enriched for polyadenylated (polyA) transcripts prior to hybridization.
2012-09-01 | E-GEOD-39684 | biostudies-arrayexpress
Project description:XMRV is a gammaretrovirus that was thought to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS) in humans until recently. The virus is culturable in various cells of human origin like lymphocytes, NK cells, neuronal cells, and prostate cell lines. MicroRNAs (miRNAs), which regulate gene expression, were so far not identified in cells infected with XMRV in culture. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection and evaluated for microRNA profile in a microarray. MicroRNA expression profiles of XMRV-infected continuous prostate cancer cell lines differ from that of virus-infected primary cells (PBLs and MDMs). miR-193a-3p and miRPlus-E1245 were observed to be specific to XMRV infection in all 4 cell types. While miR-193a-3p levels were down-regulated, miRPlus-E1245 on the other hand exhibited varied expression among the 4 cell types. The present study demonstrates that cellular microRNAs are expressed during XMRV infection of human cells. This is the first report demonstrating the regulation of miR193a-3p and miRPlus-E1245 during XMRV infection in four different human cell types.
2012-05-06 | GSE37787 | GEO
Project description:XMRV is a gammaretrovirus that was thought to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS) in humans until recently. The virus is culturable in various cells of human origin like lymphocytes, NK cells, neuronal cells, and prostate cell lines. MicroRNAs (miRNAs), which regulate gene expression, were so far not identified in cells infected with XMRV in culture. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection and evaluated for microRNA profile in a microarray. MicroRNA expression profiles of XMRV-infected continuous prostate cancer cell lines differ from that of virus-infected primary cells (PBLs and MDMs). miR-193a-3p and miRPlus-E1245 were observed to be specific to XMRV infection in all 4 cell types. While miR-193a-3p levels were down-regulated, miRPlus-E1245 on the other hand exhibited varied expression among the 4 cell types. The present study demonstrates that cellular microRNAs are expressed during XMRV infection of human cells. This is the first report demonstrating the regulation of miR193a-3p and miRPlus-E1245 during XMRV infection in four different human cell types.
2012-05-06 | GSE37786 | GEO
Project description:XMRV is a gammaretrovirus that was thought to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS) in humans until recently. The virus is culturable in various cells of human origin like lymphocytes, NK cells, neuronal cells, and prostate cell lines. MicroRNAs (miRNAs), which regulate gene expression, were so far not identified in cells infected with XMRV in culture. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection and evaluated for microRNA profile in a microarray. MicroRNA expression profiles of XMRV-infected continuous prostate cancer cell lines differ from that of virus-infected primary cells (PBLs and MDMs). miR-193a-3p and miRPlus-E1245 were observed to be specific to XMRV infection in all 4 cell types. While miR-193a-3p levels were down-regulated, miRPlus-E1245 on the other hand exhibited varied expression among the 4 cell types. The present study demonstrates that cellular microRNAs are expressed during XMRV infection of human cells. This is the first report demonstrating the regulation of miR193a-3p and miRPlus-E1245 during XMRV infection in four different human cell types. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection in duplicates and evaluated for microRNA profile in a microarray. Each test sample RNA was labeled with Hy3 and the reference pool (made by pooling all 24 test samples in each run) was labeled with Hy5.
2012-05-05 | E-GEOD-37787 | biostudies-arrayexpress
Project description:XMRV is a gammaretrovirus that was thought to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS) in humans until recently. The virus is culturable in various cells of human origin like lymphocytes, NK cells, neuronal cells, and prostate cell lines. MicroRNAs (miRNAs), which regulate gene expression, were so far not identified in cells infected with XMRV in culture. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection and evaluated for microRNA profile in a microarray. MicroRNA expression profiles of XMRV-infected continuous prostate cancer cell lines differ from that of virus-infected primary cells (PBLs and MDMs). miR-193a-3p and miRPlus-E1245 were observed to be specific to XMRV infection in all 4 cell types. While miR-193a-3p levels were down-regulated, miRPlus-E1245 on the other hand exhibited varied expression among the 4 cell types. The present study demonstrates that cellular microRNAs are expressed during XMRV infection of human cells. This is the first report demonstrating the regulation of miR193a-3p and miRPlus-E1245 during XMRV infection in four different human cell types. Two prostate cancer cell lines (LNCaP and DU145) and two primary cells (peripheral blood lymphocytes (PBLs) and monocyte-derived macrophages (MDMs)) were infected with XMRV. Total mRNA was extracted from mock- and virus-infected cells at 6, 24 and 48 hours post-infection in duplicates and evaluated for microRNA profile in a microarray. Each test sample RNA was labeled with Hy3 and the reference pool (made by pooling all 24 test samples in each run) was labeled with Hy5.
2012-05-05 | E-GEOD-37786 | biostudies-arrayexpress
Project description:This series includes 20 microarrays used to identify Xenotropic MuLV-related virus (XMRV) in a set of human prostate tumors associated with R462Q RNASEL variant (Urisman, et al. 2006). The series includes 19 prostate tumor samples (VP) and a cell line control (HeLa).
2010-07-01 | E-GEOD-3607 | biostudies-arrayexpress
Project description:Prostate cancers with clinical features of small cell prostate carcinomas (SCPC) but diverse morphologies share chemotherapy responsiveness with SCPC. We prospectively collected tumor tissues from clinically defined, morphologically diverse, aggressive variant prostate cancers (AVPCa) to determine if they also share molecular features with SCPC
2015-10-10 | GSE73902 | GEO
Project description:This series includes 20 microarrays used to identify Xenotropic MuLV-related virus (XMRV) in a set of human prostate tumors associated with R462Q RNASEL variant (Urisman, et al. 2006). Keywords: viral detection
2006-01-01 | GSE3607 | GEO
Project description:Untargeted metabolomics analyses were performed on clinically matched baseline plasma samples (n = 16 per group) prospectively collected from patients with clinically low-risk early stage prostate cancer undergoing AS who exhibited early disease progression (DP) (defined as upgrading of Gleason score (GS) and/or increased tumor volume on surveillance biopsy within 18 months after start of AS) or indolent disease (no progression for five or more years after start of AS) as well as 459 baseline plasma samples prospectively collected from patients with early-stage prostate cancer undergoing AS.
2020-05-19 | ST001408 | MetabolomicsWorkbench