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Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.
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 E-MTAB-5988.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Tzachi Hagai

PROVIDER: E-MTAB-5989 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-cell RNA-seq of of dermal fibroblasts using microfluidic droplet capture (unstimulated 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. This experiment contains data of dermal fibroblasts from 3 human individuals, unstimulated, sequenced by 10X Genomics technology. Corresponding data from stimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5989">E-MTAB-5989</a>.

2018-07-06 | E-MTAB-5988 | 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

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2018-07-06 | E-MTAB-5920 | 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. 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

RNA-seq of of dermal fibroblasts

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

ChIP-seq of H3K4me3 and H3K27ac of dermal fibroblasts

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat with and without dsRNA (poly I:C) stimulation (1ug/mL for 4 hours). 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-5918 | biostudies-arrayexpress

Re-analysis of E-MTAB-1585

Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/

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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 sequencing of LSK (lineage negative, Sca-1+, c-Kit+) cells isolated by fluorescence-activated cell sorting from the bone marrow of control young C57Bl/6Jax mice

Project description:Hematopoietic stem cells (HSCs) and different multipotent progenitor populations (MPPs) contained in the Lin- Sca-1+ c-Kit+ (LSK) compartment have previously been identified using diverse surface marker panels. However, a comprehensive and complete characterization of the complete LSK compartment is lacking to date. Here, we present a single cell RNA sequencing of LSK cells that was used to establish trajectories within the HSPC compartment. A related bulk 3’-seq study of HSCs and MPP1-4 cells was also conducted, available in the ArrayExpress database under accession number E-MTAB-7391. Another related 3’-seq study of MPP5 population is available in the ArrayExpress database under accession number E-MTAB-9135.

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RNA-seq of human whole-blood samples before and after the administration of recombinant human erythropoietin

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