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Series GSE137539 Query DataSets for GSE137539
Status Public on May 27, 2020
Title Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The full neutrophil heterogeneity and differentiation landscape remains incompletely characterized. Here we profiled more than 25,000 mouse differentiating and mature neutrophils using single-cell RNA sequencing to provide a comprehensive transcriptional landscape of neutrophil maturation, function, and fate decision in their steady state and during bacterial infection. Eight neutrophil populations (including the GMP population) were defined by distinct molecular signatures, including a new circulating mature neutrophil population highly expressing interferon-stimulated genes. The three mature peripheral blood neutrophil subsets arise from distinct maturing bone marrow neutrophil subsets, a novel mechanism that highlights the complex and precise regulation of neutrophil production. Neutrophil heterogeneity and differentiation are driven by both known and uncharacterized transcription factors. Neutrophils gradually acquire microbicidal capability as cells traverse the transcriptional landscape, representing an evolved mechanism for fine-tuned regulation of an effective but balanced neutrophil response. Bacterial infection reprograms the genetic architecture of neutrophil population, alters dynamic transition between each subpopulation, and primes neutrophils for augmented functionality without affecting overall heterogeneity. Bacterial infection-induced emergency granulopoiesis is mediated by augmented proliferation of early-stage neutrophil progenitors and accelerated post-mitotic maturation. In summary, single-cell transcriptomics enabled the reconstruction of neutrophil differentiation and maturation trajectories and uncovered neutrophil subpopulations, gene pathways, and regulators of neutrophil function and fate decisions. These data establish a reference model and general framework for studying neutrophil-related disease mechanisms, biomarkers, and therapeutic targets at single-cell resolution.
Overall design There are 10 mouse samples and 1 human sample. All relative organs consist of bone marrow (BM), peripheral blood (PB), spleen (SP), liver (LV) and peritoneal cavity (PC).
4 mouse control samples: BM sorted by cKit+ Gr1+; BM, PB, SP sorted by Gr1+.
6 mouse E. coli challenged samples: BM sorted by cKit+ Gr1+; BM, PB, SP, LV and PC sorted by Gr1+.
3 human control samples: PB sorted by CD33.
Contributor(s) Xie X, Shi Q, Wu P
Citation(s) 32719519, 38195694
Submission date Sep 16, 2019
Last update date Jan 18, 2024
Contact name Xuemei Xie
Organization name Boston Children's Hospital
Department Transfusion Medicine
Lab Luo's Lab
Street address 811 Enders Building, 320 Longwood Ave.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (13)
GSM4081545 wt_ctl_bm1
GSM4081546 wt_ctl_bm2
GSM4081547 wt_ctl_pb2
This SubSeries is part of SuperSeries:
GSE137540 Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection
BioProject PRJNA565803
SRA SRP221817

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE137539_Cell_index_Barcode.txt.gz 300.3 Kb (ftp)(http) TXT
GSE137539_Human_donor_meta.txt.gz 506.8 Kb (ftp)(http) TXT
GSE137539_Mouse_WT_Eco_meta.txt.gz 856.8 Kb (ftp)(http) TXT
GSE137539_Mouse_WT_blank_meta.txt.gz 590.0 Kb (ftp)(http) TXT
GSE137539_RAW.tar 144.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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