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Series GSE125044 Query DataSets for GSE125044
Status Public on Feb 19, 2019
Title Single cell analysis of diverse pathogen responses defines a molecular roadmap for generating antigen-specific immunity
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The immune system generates pathogen-tailored responses. The precise innate immune cell types and pathways that direct robust adaptive immune responses have not been fully characterized. By using fluorescent pathogens combined with massively parallel single cell RNA-seq, we comprehensively characterized the initial 48 hours of the innate immune response to diverse pathogens. We found that across all pathogens tested, most of the lymph node cell types and states showed little pathogen-specificity. In contrast, the rare antigen-positive cells displayed pathogen-specific transcriptional programs as early as 24 hours after immunization. In addition, mycobacteria activated a specific NK driven IFNγ response. Depletion of NK cells and IFNγ showed that IFNγ initiated a monocyte specific signaling cascade, leading to production of major chemokines and cytokines that promote Th1 development. Our systems immunology approach sheds light on early events in innate immune responses and may help further development of safe and efficient vaccines.
Overall design Transcriptional profiling of single cells from pathogen-injected mouse auricular lymph nodes, generated from deep sequencing of thousands of cells, sequenced in several batches on illumina Nextseq500. For all experiments, innate immune lymph node cells were sorted accordng to the markers indicated in Samples' Characteristics "selection marker" field into 384-well MARS-seq2.0 cell capture plates. Sorting of antigen-carrying cells (Ag+) was based on the AF488-fluorescence of the pathogens injected. Different pathogens and time points were used, as indicated in the Samples' Characteristics "infection" and "time points" fields.
Contributor(s) Blecher-Gonen R, Bost P, Hilligan KL, David E, Salam TM, Roussel E, Connor LM, Mayer JU, Halpern KB, Tóth B, Itzkovitz S, Schwikowski B, Ronchese F, Amit I
Citation(s) 30772378
Submission date Jan 14, 2019
Last update date Mar 25, 2019
Contact name Ido Amit
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (91)
GSM3561634 AB1780 (scRNA-Seq)
GSM3561635 AB1781 (scRNA-Seq)
GSM3561636 AB1782 (scRNA-Seq)
BioProject PRJNA515047
SRA SRP179081

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Supplementary file Size Download File type/resource
GSE125044_RAW.tar 54.5 Mb (http)(custom) TAR (of TXT)
GSE125044_metadata.txt.gz 256.7 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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