Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human monocyte-derived macrophages comparing healthy versus house dust mite-allergic donors

ABSTRACT: Human monocyte-derived macrophages (MDM) from HDM-allergic donors were compared to MDM from healthy donors. CD14+ monocytes were isolated from donated blood and differentiated in the presence of GM-CSF and TGFb (alveolar-like MDM) for 7 days before havest of RNA

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Julia Esser-von Bieren

PROVIDER: E-MTAB-9215 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq comparing allergen-trained versus untrained human monocyte-derived macrophages after HDM challenge

Project description:Mibrobial Patterns can induce trained innate immunity in macrophages. We tested whether innate memory can be elicited by stimulating macrophages with a house dust mite extract for 24h before washout and a resting phase of 5 days. Subsequently, macrophages were exposed to HDM for 24h and we analyzed the gene expression post-challenge.

2021-12-31 | E-MTAB-9210 | biostudies-arrayexpress

RNA-seq comparing allergen-trained versus untrained human monocyte-derived macrophages

Project description:Mibrobial Patterns can induce trained innate immunity in macrophages. We tested whether innate memory can be elicited by stimulating macrophages with a house dust mite extract for 24h before washout, and analyzed the gene expression after 5 days post-exposure.

2021-12-31 | E-MTAB-9214 | biostudies-arrayexpress

Promoter targeted histone acetylation of chromatinized parvoviral genome is essential for infrection progress

Project description:The association of host histones with parvoviral DNA is poorly understood. We analyzed the chromatinization and histone acetylation of canine parvovirus DNA during infection by confocal imaging and in situ proximity ligation assay combined with chromatin immunoprecipitation and high-throughput sequencing. We found that at late infection parvovirus replication bodies were rich in histones bearing modifications characteristic of transcriptionally active chromatin, i.e. histone H3 lysine acetylation (H3K27ac). The H3K27ac, in particular, was located in close proximity to the viral DNA-binding protein NS1. Importantly, our results show for the first time that in the chromatinized parvoviral genome, particularly the two viral promoters were rich in H3K27ac. Histone acetyltransferase (HAT) inhibitorefficiently interfered with expression of viral proteins and infection progress. Altogether, our data suggest that acetylation of histones on parvoviral DNA is essential for viral gene expression and completion of viral life cycle. Examination of H3K27 acetylation in CPV infected and non-infected NLFK (Norden laboratory feline kidney) cells. Please note that the result in this study, considering the sequencing, is the fact that the viral genome is chromatinized. Processed data in this case would be the aligned read percentages in control cells (of which 0% aligns to parvoviral genome) and infected cells (of which ~9% only aligns to parvoviral genome and not to the cat genome), which is basically the output of the read aligner software without further processing steps (no peaks or regions were identified for the associated publication). Therefore no processed data was provided, and an exception to GEO processed data requirement was made.

2016-02-11 | E-GEOD-77785 | biostudies-arrayexpress

mRNAseq of human sputum macrophages and alveolar-like monocyte-derived macrophages of healthy controls and NSAID-exacerbated respiratory disease (N-ERD) patients

Project description:NSAID-exacerbated respiratory disease (N-ERD) represents a particularly severe endotype of chronic rhinosinusitis with nasal polyps (CRSwNP), which affects around 10-16% of CRSwNP patients. N-ERD is characterized by severe and refractory nasal polyposis, bronchial asthma and intolerance to non-steroidal anti-inflammatory drugs (NSAIDs), including aspirin. Today, the pathogenesis of N-ERD remains incompletely understood and curative treatments are lacking. Macrophages are important source and target cells of arachidonic acid metabolites during type 2 inflammation, that have been neglected in N-ERD pathogenesis despite their presence in the nasal mucosa of N-ERD patients. Using a global transcriptomic approach, we identified systemic and local changes in macrophages between N-ERD patients and healthy controls. We isolated macrophages from induced sputum (sMac) and compared them to 7-days in vitro-differentiated, alveolar-like monocyte-derived macrophages (aMDM). Cells were lysed in RLT buffer with 1% beta-mercaptoethanol and stored at -80°C until RNA isolation and RNAseq. Since sMac yield of healthy controls was low, we pooled RNA of three donors (= sample S1) but excluded the data from subsequent analyses. Thus Analysis 1 shows the intra-group comparison of N-ERD sMac vs. N-ERD aMDM. In a second analysis (Analysis 2), we compared N-ERD aMDM vs. healthy control aMDM for transcriptome differences present in monocyte (blood)-derived cells.

2020-06-30 | E-MTAB-7965 | biostudies-arrayexpress

Function, targets and evolution of Caenorhabditis elegans piRNAs (mRNA)

Project description:piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans. Affymetrix mRNA expression data from wild-type and two independent prg-1;prg-2 double mutant C. elegans strains (mRNA)

2012-06-17 | E-GEOD-37432 | biostudies-arrayexpress

Gene expression analysis in mouse embryonic stem cells containing Î²-catenin lysine 49 to alanine mutation

Project description:Î²-Catenin is the major co-regulator of the Wnt signalling pathway. Î²-Catenin lysine 49 is post-translationally modified. The histone methyl transferase Ezh2 trimethylates Î²-catenin at lysine 49 and the acetyl transferase Cbp acetylates Î²-catenin at the same lysine. To determine the effects on gene expression embryonic stem cells containing either a Gfp tagged Î²-catenin wildtype (wt) or lysine 49 to alanine (K49A) loss of function mutation were analysed by micro array expression profiling. To determine the effects on gene expression in the pluripotent state two biological replicates of Gfp Î²-catenin wt and Gfp Î²-catenin K49A were analysed. The results showed that genes which affect pluripotency as well as differentiation were altered by Î²-catenin K49A mutation. To analyse the effects of gene expression during ES cell differentiation ES cells containing Gfp Î²-catenin wt or K49A were differentiated into mesodermal progenitors (mp) and neuronal progenitors (np). Two biological replicates were analysed by micro array expression profiling. Differentially expressed genes between Gfp Î²-catenin wt and K49A during differentiation were observed. Mesodermal marker genes like t-brachyury and cdx2 were not upregulated in mesodermal differentiation of Gfp Î²-catenin K49A Es cells.

2017-03-21 | E-MTAB-5523 | biostudies-arrayexpress

Total RNAseq of human healthy control inferior turbinate and glucocorticoid-treated, NSAID-exacerbated respiratory disease (N-ERD) nasal polyp nasal brushings

2020-06-30 | E-MTAB-7962 | biostudies-arrayexpress

Chromatin IP sequencing of the nuclear factor HMGB1 in livers from mice after a metabolic stress either induced by a 12-week high fat diet consumption or a fasting (6hours)-refeeding (8hours) challenge.

Project description:To unveil HMGB1 DNA occupancy in livers of mice after a metabolic stress either induced by a 12-week high fat diet consumption or a fasting (6hours)-refeeding (8hours) challenge. Challenges known to generate a robust activation of hepatic lipogenesis and liver steatosis.

2022-03-31 | E-MTAB-11543 | biostudies-arrayexpress

De-novo assembly of transcriptome from the eggs and early embrios of Astropecten Aranciacus

Project description:This work describes the molecular mechanisms of meiotic maturation and cell cycle in the starfish Astropecten Aranciacus. The study has been conducted assembling a de-novo transcriptome from the different cellular stages: oocytes, egg, zygote and early embryos. Differential expression analysis followed by rtPCR are used to assess the validity of the assembly.

2017-08-22 | E-MTAB-5679 | biostudies-arrayexpress

Bulk RNA-seq of the human malaria parasite Plasmodium falciparum 3D7 cultured under different iron conditions

Project description:Background: Host iron deficiency is protective against severe malaria as the human malaria parasite Plasmodium falciparum depends on free iron from its host to proliferate. Due to the absence of transferrin, ferritin, ferroportin, and a functional heme oxygenase, the parasite’s essential pathways of iron acquisition, storage, export, and detoxification differ from those in humans and may thus be excellent targets for therapeutic development. However, the proteins involved in these processes in P. falciparum remain largely unknown. Experimental design: To identify iron-regulated mechanisms and putative iron transporters in the human malaria parasite Plasmodium falciparum 3D7, we carried out whole-transcriptome profiling using bulk RNA-sequencing. The parasites were cultured either using erythrocytes from a donors with high, medium (healthy) or low iron status (experiment 1); or with red blood cells from another healthy donor in the presence or absence of 0.7 µM hepcidin, a specific ferroportin inhibitor and iron-regulatory hormone (experiment 2). This concentration of hepcidin was reported to reduce binding of ferrous iron to ferroportin by 50% in vitro (39). Samples from three biological replicates each were harvested at the ring and trophozoite stage (6 – 9 and 26 – 29 hours post invasion, hpi) during the second intra-erythrocytic developmental cycle under the conditions specified.

2024-04-08 | E-MTAB-13411 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data