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Series GSE137710 Query DataSets for GSE137710
Status Public on Oct 25, 2019
Title Transcriptional basis of mouse and human dendritic cell heterogeneity revealed by single-cell profiling
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to serve as a principal antigen-presenting cell type capable of initiating T cell responses. Classical dendritic cells have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells and direct their differentiation into effectors. Whilst the transcriptional features of the cDC1 subset have been well characterized, the heterogeneity of cDC2 and the development and function of distinct cell types comprising this subset remain poorly understood. Unbiased single-cell RNA sequencing analysis of DCs, combined with genetic reporter expression and fate-mapping revealed two principal cDC2 lineages, their developmental pathways and transcriptional regulators, including the expression of T-bet and RORt, two key transcription factors known to define functional adaptive and innate lymphocyte subsets. The cDC2 lineages were characterized by distinct metabolic and functional programs with phenotypic conservation observed across tissues. Extending the findings in mice to humans revealed conserved characteristics of DC heterogeneity and the presence of the newly defined DC subsets in human autoimmune disease and cancer.
Overall design Single-cell RNA sequencing was performed on mouse and human splenic dendritic cells. Two samples of mouse dendritic cells were FACS purified based on Tbx21Cre-RFP reporter expression. Single-cell RNA sequencing was also performed on CD45-positive cells in melanoma tumors from two patients.
Contributor(s) Brown CC, Gudjonson H, Pritykin Y, Deep D, Lavallee V, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe'er D, Rudensky AY
Citation(s) 31668803
Submission date Sep 19, 2019
Last update date Nov 13, 2019
Contact name Herman Gudjonson
Organization name Memorial Sloan Kettering Cancer Center
Department Computational and Systems Biology Program, SKI
Lab Dana Pe'er
Street address 417 E 68th St
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (6)
GSM4085510 Tbx21CreRFPpos
GSM4085511 Tbx21CreRFPneg
GSM4085512 human_spleen
BioProject PRJNA566350
SRA SRP222507

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Supplementary file Size Download File type/resource
GSE137710_RAW.tar 48.5 Mb (http)(custom) TAR (of TSV)
GSE137710_cell_barcodes.tsv.gz 232.6 Kb (ftp)(http) TSV
GSE137710_human_melanoma_cell_metadata_9315x14.tsv.gz 416.9 Kb (ftp)(http) TSV
GSE137710_human_melanoma_counts_normalized_9315x19445.tsv.gz 44.6 Mb (ftp)(http) TSV
GSE137710_human_spleen_cell_metadata_4465x9.tsv.gz 174.3 Kb (ftp)(http) TSV
GSE137710_human_spleen_counts_normalized_4465x12476.tsv.gz 24.7 Mb (ftp)(http) TSV
GSE137710_mouse_spleen_cell_metadata_4464x9.tsv.gz 176.7 Kb (ftp)(http) TSV
GSE137710_mouse_spleen_counts_normalized_4464x11755.tsv.gz 22.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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