Host depletion
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB24090 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We assess the mRNA-enrichment performance of a custom-made non-mRNA depletion protocol in comparison to a commercially available mRNA-enrichment kit (Ribo-off, Vazyme). Whereas most available kits focus only on removal of rRNA, our method also targets the transfer-messenger RNA (tmRNA). tmRNA was shown to consume up to 25% of the reads in RNA-sequencing data of Pseudomonas aeruginosa. Our established depletion technique is based on the targeting of overly abundant RNA species (16S and23S rRNA, tmRNA) in total RNA preparations of Pseudomonas aeruginosa PA14 by hybridization with organism-specific DNA probes and subsequent degradation by RNase H treatment. While introducing no systematic bias into the gene expression profile we were able to increase the mRNA read share of the total reads in the samples treated with our mRNA-enrichment protocol to 93% - 99%. Therefore, our custom-made depletion technique outcompeted the commercially available reference kit (72% mRNA share) and represents a cost-efficient mRNA-enrichment method for high-throughput next-generation sequencing.
2020-03-31 | GSE147748 | GEO
Project description:The aim of this work was to analyze the transcriptomic response of Buchnera aphidicola when the aphid host is submitted to depletion in essential amino acids (EAA). This treatment was combined with an increase in sucrose concentration to influence the bacterial growth rate. In this experiment, the dietary amino acids had an EAA:nonEAA ratio of either 1:1 (50% EAA) or 1:3 (25% EAA), giving low and high aphid demand of Buchnera-derived essential amino acids, respectively. This comparison was set in a 2 times 2 factorial design with sucrose concentration at 0.5 M and 1.0 M, supporting high and low aphid growth rates.
2006-04-03 | E-TABM-85 | biostudies-arrayexpress
Project description:To advance our understanding of cellular host-pathogen interactions, technologies that facilitate the co-capture of both host and pathogen spatial transcriptome information are needed. Here, we present an approach to simultaneously capture host and pathogen spatial gene expression information from the same formalin-fixed paraffin embedded (FFPE) tissue section using the spatial transcriptomics technology. We applied the method to COVID-19 patient lung samples and enabled the dual detection of human and SARS-CoV-2 transcriptomes at 55 µm resolution. We validated our spatial detection of SARS-CoV-2 and identified an average specificity of 94.92% in comparison to RNAScope and 82.20% in comparison to in situ sequencing (ISS). COVID-19 tissues showed an upregulation of host immune response, such as increased expression of inflammatory cytokines, lymphocyte and fibroblast markers. Our colocalization analysis revealed that SARS-CoV-2+ spots presented shifts in host RNA metabolism, autophagy, NFκB, and interferon response pathways. Future applications of our approach will enable new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes.
| EGAS00001006186 | EGA
Project description:The aim of this work was to analyze the transcriptomic response of Buchnera when the aphid host is submitted to a depletion of tyrosine and phenyalanine, two amino acids that are essential to its development. The data set is composed of 8 slides arranged in a dye swap experimental design. We compared Buchnera gene expression levels when aphids are reared on the control diet (AP3) versus the depleted diet (YF).
2006-03-15 | E-TABM-83 | biostudies-arrayexpress
Project description:H3 ChIP and input DNA were hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone-DNA interactions. Rapid removal of RNA polymerase II (Pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of Pol II, but rather involves a distinct mechanism linked to 3’ end formation.
2010-09-21 | GSE23778 | GEO
Project description:A comparison of epigenetic nuclear DNA methylation and gene expression changes between human dialated cardiomypathy left ventricle samples and non-failing cardiac left ventricule samples This study addresses how depletion of huaman cardiac left ventricle mitochondrial DNA and epigentic nuclear DNA methylation promote cardiac dysfunction in human dilated cardiomyopathy.
2013-06-05 | GSE43435 | GEO
Project description:Latency-associated nuclear antigen (LANA), a multifunctional protein expressed by the Kaposi sarcoma-associated herpesvirus (KSHV) in latently-infected cells, is required for stable maintenance of the viral episome. This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. LANA has also been suggested to affect host gene expression, but both the mechanism(s) and role of this dysregulation in KSHV biology remain unclear. Here we have examined LANA interactions with host chromatin on a genome-wide scale using ChIP-seq, and show that LANA predominantly targets human genes near their transcriptional start sites (TSSs). These host LANA-binding sites are generally found within transcriptionally active promoters and display striking overrepresentation of a consensus DNA sequence virtually identical to the LBS1 motif in KSHV DNA. Comparison of the ChIP-seq profile with whole transcriptome (RNA-seq) data reveals that few of the genes that are differentially regulated in latent infection are occupied by LANA at their promoters. This suggests that direct LANA binding to promoters is not the prime determinant of altered host transcription in KSHV-infected cells. Most surprisingly, the association of LANA to both host and viral DNA is strongly disrupted during the lytic cycle of KSHV. This disruption can be prevented by the inhibition of viral DNA synthesis, suggesting the existence of novel and potent regulatory mechanisms linked to either viral DNA replication or late gene expression. Profiling of KSHV LANA positioning on the host genome and examination of gene expression from promoters bound by KSHV LANA.
2014-04-01 | E-GEOD-56144 | biostudies-arrayexpress
Project description:Protein radical labeling offers an alternative analytical method for probing protein structure or protein interaction with other bio-molecules. Since the Fast Photochemical Oxidation of Proteins has already shown its essential role in studying biomolecular as-semblies and it was successfully adopted to characterize the interaction of transcription factor and its DNA response element, we initiated an experiment to investigate the benefits of isotopic depletion on analyzing the singly oxidized protein by Top-Down mass spectrometry. The complex of FOXO4 DNA-binding domain (FOXO4-DBD) and Insulin Response Element (IRE) was se-lected a model biological system. To overcome limitations of top-down technology which encounters predominantly with its spec-tra complexity, we prepared an isotopically depleted (ID) version of FOXO4-DBD alongside to the isotopically natural one (IN) to study the interaction. For the first time, depleted protein was used to quantify the extent of modification of covalently labelled protein. Comparing tandem mass spectra of natural and depleted proteins, increased signal-to-noise ratio gives arise to more frag-ment ions suitable for quantification and subsequently enhances the sequence coverage of 19 %. Such improvement in the frag-ment ions detection enables to detect additional 21 oxidized residues compered to non-depleted sample. Moreover, less common modifications are detected including formation of keto forms and lysine carbonylation. Moreover, the comparison of Top-Down depleted data and bottom-up results displays high consistency and complementarity of both techniques, shedding a light on tran-scription factor and DNA-response element complex formation. Thus, we believe that our study emphasizes the potential of iso-topic depletion for quantitative top-down proteomics.
2024-01-26 | PXD044447 | Pride
Project description:The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes accumulation of local H3K9me2, and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. ChIP timecourse experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly-synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion. Examination of transcription factor occupancy in cells with newly synthesized Oct4.
2015-01-23 | E-GEOD-65192 | biostudies-arrayexpress
Project description:A comparison of epigenetic nuclear DNA methylation and gene expression changes between human dialated cardiomypathy left ventricle samples and non-failing cardiac left ventricule samples This study addresses how depletion of huaman cardiac left ventricle mitochondrial DNA and epigentic nuclear DNA methylation promote cardiac dysfunction in human dilated cardiomyopathy. Each sample was fluorescently labeled and hybridized to Roche Nimblegen 2.1M Deluxe Promoter Arrays and Expression arrays.
2013-06-05 | E-GEOD-43435 | biostudies-arrayexpress