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

Bulk RNA-seq of of bone marrow derived mononuclear phagocytes

ABSTRACT: Dermal fibroblasts from mouse, rat, rabbit and pig, stimulated with LPS, with dsRNA (poly I:C), and controls.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Sus scrofa

SUBMITTER: Tzachi Hagai

PROVIDER: E-MTAB-6773 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Gene expression variability across cells and species shapes innate immunity.

Hagai Tzachi T Chen Xi X Miragaia Ricardo J RJ Rostom Raghd R Gomes Tomás T Kunowska Natalia N Henriksson Johan J Park Jong-Eun JE Proserpio Valentina V Donati Giacomo G Bossini-Castillo Lara L Vieira Braga Felipe A FA Naamati Guy G Fletcher James J Stephenson Emily E Vegh Peter P Trynka Gosia G Kondova Ivanela I Dennis Mike M Haniffa Muzlifah M Nourmohammad Armita A Lässig Michael M Teichmann Sarah A SA

Nature 20181024 7730

As the first line of defence against pathogens, cells mount an innate immune response, which varies widely from cell to cell. The response must be potent but carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here we characterize the innate immune response's transcriptional divergence between species and variability in expression among cells. Using bulk and single-cell transcriptomics in fibroblasts and mononuc ...[more]

PMID: 30356220

Similar Datasets

Bulk RNA-seq of of human dermal fibroblasts from up to 66 individuals (supplementary)

Project description:Dermal fibroblasts from up to 66 human donors, stimulated with dsRNA (poly I:C) in a time course of 0, 2, 6 hours, profiled using the Smart-seq2 protocol. Donor fibroblast samples were supplied by the Hipsci consortium.

2018-07-16 | E-MTAB-7032 | biostudies-arrayexpress

RNA-seq of of dermal fibroblasts

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat, stimulated with dsRNA (poly I:C), interferon and controls.<br>The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-5919 | biostudies-arrayexpress

Single-cell RNA-seq of of bone marrow derived mononuclear phagocytes derived from mouse; rat; rabbit or pig

Project description:Bone marrow derived phagocytes from mouse, rat, rabbit and pig stimulated with LPS (100ng/mL) or with dsRNA (poly I:C) (1ug/mL) for 0,2,4,6 hours. Processed files include UMI matrices of QCed cells that belong to the first cluster (as described in the publication), which were used for all the analyses presented in the publication.

2018-07-16 | E-MTAB-6754 | biostudies-arrayexpress

Single-cell RNA-seq of of dermal fibroblasts (supplementary - human fibroblasts stimulation with dsRNA)

Project description:Dermal fibroblasts from human, stimulated with dsRNA (poly I:C) in a time course of 0, 2, 6 hours, profiled using the Smart-seq2 protocol

2018-07-16 | E-MTAB-7037 | biostudies-arrayexpress

RNA-seq of fibroblasts from two bat species stimulated by dsRNA to trigger antiviral response

Project description:Dermal fibroblasts from megabat and microbat, stimulated with dsRNA (poly(I:C)) and controls. Bats can harbor some of the most deadliest viruses to humans while rarely displaying pathogenicity themselves. To study their innate immune response - the expression program that is initiated once a pathogen is senseds, we stimulated dermal fibroblast cells from two species (Rousettus aegyptiacus and Pipistrellus kuhlii) for four hours with dsRNA - a viral RNA mimic that triggers a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq.

2022-10-01 | E-MTAB-10870 | biostudies-arrayexpress

Single-cell RNA-seq of of dermal fibroblasts (second replicate)

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat, stimulated with dsRNA (poly I:C) in a time course of 0,4 and 8 hours, profiled using the Smart-seq2 protocol.<br>The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-6066 | biostudies-arrayexpress

Single-Cell RNA-seq of bat and human fibroblasts stimulated by dsRNA to trigger antiviral response

Project description:Dermal fibroblasts from bat and human, stimulated with dsRNA (poly(I:C)) and controls. Bats can harbor some of the most deadliest viruses to humans while rarely displaying pathogenicity themselves. To study the transcriptional divergence and cell-to-cell variability of their innate immune response - the expression program that is initiated once a pathogen is sensed, we stimulated dermal fibroblast cells from Rousettus aegyptiacus and from human for four hours with dsRNA - a viral RNA mimic that triggers a rapid innate immune response. Subsequently, we profiled the response using scRNA-seq.

2022-10-01 | E-MTAB-11056 | biostudies-arrayexpress

Single-cell RNA-seq of of dermal fibroblasts using microfluidic droplet capture (stimulated cells)

Project description:The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.<br>This experiment contains data of dermal fibroblasts from 3 human individuals, stimulated with dsRNA (poly I:C) for 6 hours, sequenced by 10X Genomics technology. Corresponding data from unstimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5988">E-MTAB-5988</a>.

2018-07-06 | E-MTAB-5989 | biostudies-arrayexpress

single-cell RNA-seq of of dermal fibroblasts

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat, stimulated with dsRNA (poly I:C) in a time course of 0,2,4 and 8 hours, profiled using the Smart-seq2 protocol.<br>The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-5920 | biostudies-arrayexpress

Priming by IKKβ recruits NLRP3 to the trans-Golgi network to enable NEK7-independent inflammasome activation

Project description:The NLRP3 inflammasome plays a central role in antimicrobial defense as well as in the context of sterile inflammatory conditions. NLRP3 activity is governed by two independent signals: The first signal primes NLRP3, rendering it responsive to the second signal, which then triggers inflammasome formation. Our understanding of how NLRP3 priming contributes to inflammasome activation remains limited. Here we show that IKKβ, a kinase activated during priming, induces recruitment of NLRP3 to phosphatidylinositol-4-phosphate (PI4P), a lipid enriched on the trans-Golgi network. Intriguingly, NEK7, a mitotic spindle kinase that had previously been thought to be indispensable for NLRP3 activation, was redundant for inflammasome formation when IKKβ recruited NLRP3 to PI4P. Studying iPSC-derived human macrophages revealed that the IKKβ-mediated NEK7-independent pathway constitutes the predominant NLRP3 priming mechanism in human myeloid cells. Our results suggest that PI4P binding represents a new type of "primed" state into which NLRP3 is brought by IKKβ activity.

2022-11-17 | PXD035302 | Pride

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