Common and ancestral histone patterns in newly identified human cellular structures.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Liver
DISEASE(S): Hepatitis
SUBMITTER: 
Dan Maloney
LAB HEAD: Lusi Elena Angela
PROVIDER: PXD004986 | Pride | 2017-03-03
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 150219A_Lusi_4A.mzxml | Mzxml | |||
| 150219A_Lusi_4B.mzxml | Mzxml | |||
| peptides.pep.xml | Pepxml |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Acanthamoeba-infecting Mimiviridae belong to three clades: Mimiviruses (A), Moumouviruses (B) and Megaviruses (C). The uniquely complex mobilome of these giant viruses includes virophages and linear 7 kb-DNA molecules called “transpovirons”. We recently isolated a new virophage (Zamilon vitis) and two new transpovirons (maBtv and mvCtv) respectively associated to B-clade and C-clade Mimiviridae. We used the capacity of the Zamilon virophage to replicate both on B-clade and C-clade host viruses to investigate the three partite interaction network governing the propagation of transpovirons. We notably performed proteomic comparisons of host viruses and virophage particles carrying or cleared of transpovirons in search of proteins involved in this adaptation process. These experiments revealed that transpoviron-encoded proteins are synthetized during the combined Mimiviridae/virophage/transpoviron replication process and are specifically incorporated into the virophage and Mimiviridae virions together with the cognate transpoviron DNA. This is a unique example of intricate commensalism in the viral world, where the Zamilon virophage and the transpoviron depend on their host giant virus to replicate, and the transpoviron depends on the virophage to propagate from one host virus to another.
2020-04-14 | PXD009037 | Pride
Project description:The differentiation of specialized feeding sites in Arabidopsis root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Arabidopsis root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation. Samples, collected 14 days post infestation, consisted of three biological replicates per treatment (control root cells or giant cells). RNA samples were isolated from ~150 control cells or from ~80 giant cells using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA amplifications were carried out with the NuGEN WT-Ovation Pico kit. GSM546568-GSM546577: Control and giant cells collected 21 days post infestation.
2012-04-26 | E-GEOD-37553 | biostudies-arrayexpress
Project description:Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser capture microdissection. Arabidopsis root cells undergoing giant cell formation due to nematode infestation and un-infested control root cells were laser captured and used to evaluate 2 amplification systems. One, NuGEN's WT-Ovation Pico amplification system, uses total RNA as starting material while the other, NuGEN's WT-One-Direct Amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The NuGEN WT-Ovation One-Direct system was less reproducible and more variable than the NuGEN WT-Ovation Pico system. The NuGEN WT-Ovation Pico Amplification kit resulted in the detection of thousands of genes differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the NuGEN WT-Ovation One-Direct Amplification kit. Evaluation of each amplification system consisted of three biological replicates per treatment (control root cells or giant cells) with one biological replicate split into three technical replicates for a total of 10 samples per amplification procedure. RNA samples for amplification with the NuGEN WT-Ovation Pico kit were isolated from 150 control cells or from 80 giant cells using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). For amplification with the NuGEN WT-Ovation One-Direct kit, samples containing 150 control or 80 giant cells were collected directly into 2ul of the NuGEN lysis buffer. RNA amplifications were carried out according to the respective kitsâ?? protocols.
2010-06-08 | E-GEOD-21981 | biostudies-arrayexpress
Project description:Expression profiling of wild-type and Prdm1 null mouse trophoblast giant cell cultures using Illumina whole genome mouse V2 arrays. The hypothesis tested was that Prdm1/Blimp1 regulates expression of genes required for spiral artery trophoblast giant cell function. Prdm1 null and littermate control wild-type trophoblast stem cell clones were generated from blastocyst outgrowths. Total RNA was obtained from multiple replicates of four wild-type TS cell clones and four Prdm1 null TS cell clones differenitated for zero, two, four and six days by growth factor withdrawal and hybridized to Illumina WG6_V2 arrays
2016-03-14 | E-GEOD-74409 | biostudies-arrayexpress
Project description:We characterized the mouse trophoblast giant cell epigenome and gene expression profiles. We then compared these data to our data on underrepresentation in the polyploid trophoblast giant cells. We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles (3' RNA-Seq) for trophoblast giant cells derived from mouse. Furthermore, we profiled digital expression profiles (3' RNA-Seq) for in vivo trophoblast giant cells samples from e9.5 wildtype mouse trophoblast giant cells. We found that underrepresented domains in trophoblast giant cells are enriched for repressive marks and anti-correlate with active marks and transcription.
2014-05-29 | E-GEOD-50561 | biostudies-arrayexpress
Project description:The differentiation of specialized feeding sites in Zea mays root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Zea mays root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation. Each time point (14 day and 21 day) consisted of three biological replicates per treatment (control root cells or giant cells). Control cells were captured from an area ~13,000,000 um2 in size and giant cells were captured from an area ~5,000,000 um2 in size. RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA amplifications were carried out with the NuGEN WT-Ovation Pico kit.
2012-04-27 | E-GEOD-37556 | biostudies-arrayexpress
Project description:Nested parasitic chains are common schemes in nature, not limited to cellular organisms. Some giant viruses infecting protists are hyperparasitized by smaller viruses named virophages. Both can carry episomal plasmid-like DNA molecules known as transpovirons in their particles. They all share common transcriptional regulatory elements dictating the expression of their genes, which are transcribed within viral factories built by giant viruses in the host cytoplasm. This suggests close but as yet undetermined interactions between their respective transcriptional networks. Here, we studied the protein content of Megavirus chilensis virions produced in Acanthamoeba castellanii cells co-infected or not with the virophage Zamilon vitis.
2024-09-03 | PXD052049 | Pride
Project description:It is well established that the pathogenicity and pathology of rabies virus (RABV) varies according to the variant, but the exact mechanism for this is still not completely known. In this study, the gene expression profile in brains of mice infected with virus isolated from a human case of dog rabies (V2) or vampire bat-acquired rabies (V3) were analyzed in experimental condition. In total, 138 array probes associated with 120 genes were differentially expressed between mice inoculated with V2 and the control mice at day 10 post-inoculation. A single probe corresponding to an unannotated gene was identified in V3 versus control mice. Gene ontology (GO) analysis revealed that all of the genes up-regulated in mice inoculated with V2 were involved in the biological process of immune defense against pathogens. Although both variants being considered pathogenic, inoculation in exactly same condition generated particular results regarding gene expression, more likely to differences in pathogenesis between dog and bat-related variants, already considered in other studies. This study was the first to demonstrate the global gene expression in experimental rabies infection due to V3 wild-type rabies virus, which reservoir is the vampire bat Desmodus rotundus, an important transmitter of rabies for humans and production animals in Latin America.
2022-02-28 | E-MTAB-11414 | biostudies-arrayexpress
Project description:The Chinese giant salamander (CGS, Andrias davidianus) is the largest and longest-lived amphibian. Global and quantitative proteome analysis of multiple tissues would indicate tissue-specific mechanisms and investigate the function of each protein from a whole-organism perspective. Herein, this study performed proteome analysis of eleven tissues collected from adult female CGS using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS methods. Based on the predicted protein database from CGS transcriptome database previously obtained, we identified a total of 4607 proteins with quantitative information. Among them, 2153 proteins were shared by two iTRAQ 8-plex experiments with liver as common sample, and these proteins were used for subsequent analysis. Our data will be useful for future research into this large-genome species, as well as for vertebrate-wide comparative genomic, transcriptomic and proteomic studies.
2019-11-18 | PXD005648 | Pride
Project description:Biotrophic plant pathogens have evolved sophisticated strategies to manipulate their host. They derive all of their nutrients from living plant tissues, by making intimate contact with their host while avoiding a resistance response. Rice is one of the most important crop plants worldwide and an excellent model system for studying monocotyledonous plants. Estimates of annual yield losses due to plant-parasitic nematodes on this crop range from 10 to 25% worldwide. One of the agronomically most important nematodes attacking rice is the rice root knot nematode Meloidogyne graminicola. Attack of plant roots by sedentary plant parasitic nematodes, like the root knot nematodes (RKN; Meloidogyne spp.) involves the development of specialized feeding cells in the vascular tissue. The second stage juvenile of the RKN punctures selected vascular cells with its stylet, injects pharyngeal secretions, and this ultimately leads to the reorganisation of these cells into typical feeding structures called giant cells (GCs), from which the nematode feeds for the remainder of its sedentary life cycle (Gheysen & Mitchum, 2011). Morphological and physiological reprogramming of the initial feeding cell leads to nucleus enlargement, proliferation of mitochondria and plastids, metabolic activation, cell cycle alterations and cell wall changes (Gheysen and Mitchum, 2011). The hyperplasia and hypertrophy of the surrounding cells leads to the formation of a root gall, which is typically formed at the root tips in the case of the rice RKN M. graminicola. In comparison with other RKN, M. graminicola has a very fast life cycle, with swelling of the root tips observed as early as 1 day after infection (dai). At 3 dai, terminal hook-like galls are clearly visible (Bridge et al., 2005). After 3 moults the nematodes are mature, around 10 dai. The M. graminicola females lay their eggs inside the galls, while most other RKN deposit egg masses at the gall surface, and hatched juveniles can reinfect the same or adjacent roots. In well-drained soil at 22-29 degrees C the life cycle of M. graminicola is completed in 19 days. 2 biological replicates of nematode infected giant cells and control vascular cells were sampled at two time points: 7 and 14 dai
2013-08-07 | E-GEOD-43577 | biostudies-arrayexpress