Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJEB22024: Single-cell RNA-seq of of dermal fibroblasts

Source: EBI / ERA1979729
Submission Date: Jul 7 2018
Release Date: Jul 7 2018
Update Date: Jul 7 2018

Summary: 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.

Overall Design: 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.

GEN Datasets:
GEND000230 GEND000231
Strategy:
Species:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Single-cell RNA-seq of of dermal fibroblasts
Library Construction 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.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -; Reverse
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Unspecific; Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Gene expression variability across cells and species shapes innate immunity.
Nature . 2018-10-24 [PMID: 30356220]