GFP pulldown for the RiboVD project
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Cercopithecus Aethiops (green Monkey) (grivet) Homo Sapiens (human)
TISSUE(S): Cell Culture
SUBMITTER: 
Eszter Kassa
LAB HEAD: Ylva Ivarsson
PROVIDER: PXD033874 | Pride | 2023-03-09
REPOSITORIES: Pride
Similar Datasets
Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008). For this study, 4 experimental Virochip microarrays derived from tissue and swabs from affected titi monkeys were analyzed. We also used 18 Virochip microarrays derived from sera from healthy random human blood donors as a negative background set for Z-score analysis (see Chiu, et al., Clin Infect Dis, 2006). Raw Agilent microarray .txt files are background normalized and the 19,058 70-mer viral probes are then selected and displayed as columns in the processed data table.
2011-02-05 | E-GEOD-26898 | biostudies-arrayexpress
Project description:In this study, we pull-down human Talin1-GFP and GFP from U2OS cells plated on fibronectin. Binding partners were then analysed using mass-spectrometry.
2021-05-12 | PXD024634 | Pride
Project description:In this study, we pull-down human TLNRD1-GFP and GFP from HEK cells. Binding partners were then analysed using mass-spectrometry.
2024-01-27 | PXD045258 | Pride
Project description:During HIV-1 infection, there is a massive perturbation of host gene expression, but as yet, genome-wide studies have not identified host genes affecting HIV-1 replication in lymphatic tissue, the primary site of virus-host interactions. In this study, we isolated RNA from the inguinal lymph nodes of 22 HIV-1-infected individuals and utilized a microarray approach to identify host genes critically important for viral replication in lymphatic tissue by examining gene expression associated with viral load. Strikingly, ~95% of the transcripts (558) in this data set (592 transcripts total) were negatively associated with HIV-1 replication. Genes in this subset (1) inhibit cellular activation/proliferation (ex.: TCFL5, SOCS5 and SCOS7, KLF10), (2) promote heterochromatin formation (ex.: HIC2, CREBZF, ZNF148/ZBP-89), (3) increase collagen synthesis (ex.: PLOD2, POSTN, CRTAP), and (4) reduce cellular transcription and translation. Potential anti-HIV-1 restriction factors were also identified (ex.: NR3C1, HNRNPU, PACT). Only ~5% of the transcripts (34) were positively associated with HIV-1 replication. Paradoxically, nearly all these genes function in innate and adaptive immunity, particularly highlighting a heightened interferon system. The predominance of negative correlations as well as the disconnect between host defenses and viral load point to the importance of genes that regulate target cell activation and genes that code for potentially new restriction factors as determinants of viral load rather than conventional host defenses. Total RNA was isolated from the inguinal lymph nodes of 22 HIV-1-infected subjects at different clinical stages (and varying viral loads) and prepared for RNA extraction and hybridization on Affymetrix Human Genome U133 Plus 2.0 microarrays. Replicate arrays were performed for lymph node samples to minimize assay noise and host genes critically important for viral replication in lymphatic tissue were identified by examining gene expression and its association with viral load. Replicates were not performed for samples WB91 and TS35 due to limited amounts of biomaterial.
2010-06-08 | E-GEOD-21589 | biostudies-arrayexpress
Project description:Epstein-Barr Virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B-lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B-cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration. Six sequencing experiments were performed. One EBNA1 ChIP-seq was controlled with IgG ChIP-seq. Two MNase-seq biological replicates were each conrolled by input seq using the same cells subjected to MNase digestion.
2012-08-28 | E-GEOD-39913 | biostudies-arrayexpress
Project description:Gamma-herpesviruses encode a cytoplasmic mRNA-targeting endonuclease, termed SOX, that cleaves the majority of mRNAs within a cell. Cleaved fragments are subsequently degraded by the cellular mRNA degradation machinery. Here, we reveal that mammalian cells respond to this widespread cytoplasmic mRNA decay by altering levels of RNA polymerase II (RNAPII) transcription in the nucleus. Measurements of both RNAPII recruitment to promoters and nascent mRNA synthesis revealed that the majority of affected genes are transcriptionally repressed in SOX-expressing cells. The transcriptional feedback does not occur in response to the initial endonuclease-induced cleavage, but instead to degradation of the cleaved fragments by cellular exonucleases. In particular, Xrn1 catalytic activity is required for transcriptional repression. Notably, viral mRNA transcription escapes decay-induced repression, and this escape requires Xrn1. Collectively, these results indicate that mRNA decay rates impact transcription in mammalian cells, and that gamma-herpesviruses have incorporated this feedback mechanism into their own gene expression strategy. NIH 3T3 cells were mock, WT, or ∆HS infected with MHV68 in duplicate and 4sU-labeled RNA isolated. 4sU-labeled RNA was submitted for sequencing and reads aligned to the mouse genome or MHV68 viral genome. Differential cellular gene expression was determined between mock and WT infected, mock and ∆HS infected, as well as differential viral gene expression between WT and ∆HS.
2015-07-23 | E-GEOD-70481 | biostudies-arrayexpress
Project description:Diagnosis of acute respiratory viral infection is currently based on clinical symptoms and pathogen detection. Use of host peripheral blood gene expression data to classify individuals with viral respiratory infection represents a novel means of infection diagnosis. We used microarrays to capture peripheral blood gene expression at baseline and time of peak symptoms in healthy volunteers infected intranasally with influenza A H3N2, respiratory syncytial virus or rhinovirus. We determined groups of coexpressed genes that accurately classified symptomatic versus asymptomatic individuals. We experimentally inoculated healthy volunteers with intranasal influenza, respiratory syncytial virus or rhinovirus. Symptoms were documented and peripheral blood samples drawn into PAXgene tubes for RNA isolation.
2009-08-06 | E-GEOD-17156 | biostudies-arrayexpress
Project description:Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the dataset. We present evidence to suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light of our results, the overall contribution of perfectly base paired double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to define a more comprehensive scenario of vsRNA biogenesis and their regulatory functions in plants Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE16996 10 samples examined: Arabidopsis plants infected with TRV, TuMV or CMV; Nicothiana benthamiana plants infected with CymRSV, PVX or PMMoV; Cucumis melo plants infected with MNSV, quimeric MNSV or WMV and Solanum lycopersicum plants infected with TYLCV.
2009-07-09 | E-GEOD-16996 | biostudies-arrayexpress
Project description:Efficient virus replication in its vector, Aedes mosquitoes, is essential for the transmission of arboviral diseases like dengue virus (DENV) in populations. In order to identify RNA-independent host factors involved in DENV replication in mosquitoes, we established a system expressing all non-structural proteins within the context of the macro protein complex as observed during viral infections. We GFP-tagged Loqs to purify it's interactors by label-free mass spectrometry.
2022-08-10 | PXD035419 | Pride
Project description:We report the cloning and sequencing of both endogenous small RNAs and virus-derived siRNAs produced by the antiviral RNAi pathway in Drosophila. We find that a diverse panel of viruses are targeted by the RNAi pathway in Drosophila to produce abundant virus-derived siRNAs, and these siRNAs map to various locations within the viral genomes. Knockdown of various RNAi and miRNA pathway components alters the levels of these viral small RNAs. Drosophila DL1 cells were treated with dsRNA for 3 days to deplete factors involved in the antiviral RNAi pathway and miRNA pathway, then were challenged with one of four viruses for 4 days. Total RNA was collected, and the small RNA populations from 15-29 nt were cloned and sequenced.
2013-01-01 | E-GEOD-43031 | biostudies-arrayexpress