E-MTAB-5920 - Single-cell RNA-seq of dermal fibroblasts stimulated with dsRNA (poly I:C) in a time course of 0, 2, 4 and 8 hours

Released on 6 July 2018, last updated on 4 June 2019
Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus
Samples (1180)
Protocols (5)
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.
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.
Experiment types
RNA-seq of coding RNA from single cells, species design, stimulus or stress design, time series design
Gene expression variability across cells and species shapes innate immunity. Tzachi Hagai, Xi Chen, Ricardo J. Miragaia, Raghd Rostom, Tomás Gomes, Natalia Kunowska, Johan Henriksson, Jong-Eun Park, Valentina Proserpio, Giacomo Donati, Lara Bossini-Castillo, Felipe A. Vieira Braga, Guy Naamati, James Fletcher, Emily Stephenson, Peter Vegh, Gosia Trynka, Ivanela Kondova, Mike Dennis, Muzlifah Haniffa, Armita Nourmohammad, Michael Lässig & Sarah A. Teichmann. , PMID:30356220
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-5920.idf.txt
Sample and data relationshipE-MTAB-5920.sdrf.txt