E-MTAB-4388 - Single-cell RNA-sequencing resolves a CD4+ T cell fate bifurcation

Status
Submitted on 24 November 2014, released on 21 March 2017, last updated on 22 March 2017
Organism
Mus musculus
Samples (1598)
Protocols (4)
Description
Single-cell RNA sequencing (scRNA-seq) was used to study the various transcriptional states of individual CD4+ T cells during blood-stage Plasmodium chabaudi infection in mice. This is an experimental model of malaria in which CD4+ T cells are essential for controlling parasite numbers, and which is characterized by concurrent development of Th1 and Tfh cells. We have used Plasmodium-specific TCR transgenic CD4+ T cells to minimise the effects of TCR diversity on Th fate decisions. Activated antigen-specific cells were studied at days 0, 2, 3, 4 and 7. In addition, dendritic cells and monocytes were studied at days 0 and 3. Cell lysis, RT and cDNA preamplification was performed using Fluidigm C1 system.
Experiment types
RNA-seq of coding RNA from single cells, development or differentiation design
Contact
Citation
Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria. Tapio Lönnberg, Valentine Svensson, Kylie R. James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S. F. Soon, Lily G. Fogg, Arya Sheela Nair, Urijah N. Liligeto, Michael J. T. Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D. Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T. Bunn, Christian R. Engwerda, William R. Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, and Sarah A. Teichmann.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-4388.idf.txt
Sample and data relationshipE-MTAB-4388.sdrf.txt
Links