E-MTAB-3649
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD001805MSV000080750
PROVIDER: E-MTAB-3649 | ExpressionAtlas | 2019-05-14
REPOSITORIES: ExpressionAtlas
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Project description:In the context of studying visceral leishmaniasis, neutrophils infected with Leishmania donovani have been compared to uninfected neutrophils. Compared time points are 0, 6 and 24 hours post infection. Neutrophils of three human donors have been used. Overall 6 samples for infected neutrophils at time point 6 hours and 6 samples for infected neutrophils at time point 24 hours exist, including three biological samples and two technical samples. Uninfected neutrophils represent 3 samples at time point 0 hours, 3 samples at time point 6 hours and 3 samples at time point 24 hours. Transcriptome of Leishmania donovani culture has been assessed in two replicates.
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Project description:To elucidate miRNA-mediated temporal crosstalk during productive infection, we identified genome-wide miRNA target sites using Argonaute-crosslinking and immunoprecipitation followed by high-throughput sequencing (AGO-CLIPseq) in human cytomegalovirus (HCMV)-infected cells and evaluated the targeting efficacy by applying our new AGO-CLIPseq enrichment (ACE)-scoring algorithm. To uncover the miRNA targetome in uninfected or infected human foreskin fibroblasts with HCMV (24, 48 and 72 post-infection hour) were subjected to take AGO-CLIPseq as well as mRNAseq/smallRNAseq.
2014-12-03 | E-GEOD-63797 | biostudies-arrayexpress
Project description:mircoRNAs (miRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of miRNAs in ST cells uninfected or infected by PDCoV by high-throughput sequencing
2021-11-04 | GSE176550 | GEO
Project description:Purpose: When we infect MDCK epithelial cells we low dosage of Listeria monocytogenes we observe that at late times (24 h) post infection that infected cells pertaining in infection foci get collectively extruded out of the epithelial monolayer forming a 3D mound. The formation of the infection mound results from the competition between two populations: the uninfected cells ("surrounders") that eventually squeeze and extrude the infected cells ("mounders"). Using RNA-Sequencing, we performed gene expression profiling for uninfected MDCK cells, cells infected for 24 h with Listeria monocytogenes at an MOI of 200 (both "mounders" and "surrounders") and cells sorted to infected ("mounders") or uninfected ("surrounders") populations after being infected for 24 h with Listeria monocytogenes. Our goal was to understand how transcriptional regulation leads to the collective extrusion of infected epithelial cells triggered by surrounding uninfected cells. Methods and Results: By analyzing the differentially expressed genes between all conditions we find a significant number of up- or down-regulated genes between all groups. Through pathway enrichemnet analysis we find that compared to cells not exposed to infection "mounders" showed significant downregulation in 31 genes related to tight junctions and ZO-1 was one of the key genes downregulated and to a lesser degree to pathways related to adherens junctions, focal adhesions and regulation of the actin cytoskeleton. "Surrounders" showed significant downregulation to genes related to actin cytoskeleton, to endocytosis to ahderens junctions and to a lesser degree focal adhesions and tight junctions. Especially "surrounders" and to a lesser degree "mounders" showed upregulation on IL-17 and NF-kB and TNF related signaling pathways, which underlines the fact that although "surrounders" are uninfected their distinct mechanical behavior might arise from cytokines released from "mounders" which impact crucially their phenotype. Interestingly "mounders" only showed additionally upregulation on DNA replication, cell cycle related pathways and ferroptosis suggesting that these cells might be undergoing some kind of stress response. Conclusions: Infection of MDCK epithelial cells with Listeria monocytogenes significantly alters the transcriptome of the infected host cells when those are examined 24 h post infection. Both infected and uninfected cells in an infected well show significant transcriptomic changes compared to uninfected cells but also compared to each other. Most importnantly innate immunity related pathways are singificanlty upregulated for un infected cells in an infected well and to a lesser degree for infected cells as compared to cells not exposed to infection.
2019-11-19 | GSE140626 | GEO
Project description:Circular RNAs (circRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of circRNAs in swine testicular (ST) cells uninfected or infected by PDCoV by high-throughput sequencing.
2021-11-04 | GSE147188 | GEO
Project description:SILAC labeled human kidney cells (293 cells) or bat kidney cells (PakiT03cells)were infected with Hendra virus for 8 or 24 hours and compared to uninfected control cells. Protein identification and quantitation relied on a combination of Uniprot lists of proteins and Proteomics Informed by Transcriptomics (PIT) analysis whereby RNA extracted from the same samples was deep sequenced and the sequencing data was used to construct mRNA from which possible ORFS were inferred and used as a search space by MaxQuant.
2014-11-05 | PXD001165 | Pride
Project description:SILAC labeled human kidney cells (293 cells) or bat kidney cells (PakiT03cells)were infected with Hendra virus for 8 or 24 hours and compared to uninfected control cells. Protein identification and quantitation relied on a combination of Uniprot lists of proteins and Proteomics Informed by Transcriptomics (PIT) analysis whereby RNA extracted from the same samples was deep sequenced and the sequencing data was used to construct mRNA from which possible ORFS were inferred and used as a search space by MaxQuant.
2016-06-17 | MSV000079832 | MassIVE
Project description:Smal RNA is a type of single-stranded small-molecule RNA with a size of about 18-40 bases, mainly including microRNA, piRNA, snoRNA, snRNA, tRNA and so on. Small RNAs have important regulatory functions in cells and have the potential to be used as disease diagnostic markers or drug targets. We report the results of all small RNAs in exosomes from HTNV infected/uninfected HUVECs by high-throughput sequencing technology. We find that the transcriptomes of Exo-NC group (exosomes from HTNV uninfected cells) and Exo-HV group (exosomes from HTNV infected cells) expressed distinctly different expression patterns of miRNA.
2023-03-19 | GSE147257 | GEO
Project description:a high-throughput Illumina/Solexa sequencing was conducted, 478262, 702593, 835394 and 894277 unique sRNAs was discovered from four periods of M. robertsii infection, uninfected (0h), infected for 12h, 24h and 36h. Then, 7, 7, 6 and 7 known pre-miRNAs were obtained, and 33, 58, 54 and 52 candidate novel miRNAs was detected in four periods. Further analysis showed that 24 of those candidate novel miRNAs were matched to other known insect miRNAs, while 36 of those miRNAs lacked sequence homologues of insect organisms.
2022-04-01 | GSE99322 | GEO
Project description:mRNA profiles of astrocytes infected with Borrelia burdorferi for 24 hours, 48 hours, and 24 hour uninfected controls were generated by deep sequencing, in triplicate, using Illumina HiSeq.
2017-02-01 | GSE85143 | GEO