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Series GSE150719 Query DataSets for GSE150719
Status Public on Apr 12, 2021
Title Molecular tracking devices quantify antigen distribution and archiving in the lymph node.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary Live, attenuated vaccines generate humoral and cellular immune memory, increasing the duration of protective immune memory. We previously found that antigens derived from vaccination or viral infection persist beyond infection clearance via acquisition and retention (“archiving”) in lymphatic endothelial cells (LECs). Archived antigen maintains an effector-like pool of antigen-specific memory T cells, enhancing clearance of subsequent infections. Technical limitations of fluorescent labeling have precluded a complete picture of antigen archiving across cell types in lymph tissue. We developed a “molecular tracking device” to follow the distribution, acquisition, and retention of antigen in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance across major cell types in the lymph node two weeks later, validating its acquisition by migratory dendritic cells and durable retention by LECs and unexpected stromal cell types. Variable antigen levels in LECs enabled the identification and validation of caveolar endocytosis as a mechanism of antigen acquisition. Molecular tracking devices enable new approaches to study dynamic tis-sue dissemination at cellular resolution in vivo.

We developed a 'molecular tracking device' to follow the distribution, acquisition, and retention of antigen across cell types in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance in immune and stromal cell types two weeks later, validating its retention by LECs and transfer to migratory dendritic cells and defining new reservoirs of archived antigen in stromal cells. Molecular tracking devices broadly enable new approaches to study molecular dissemination and retention in live animals.
 
Overall design Single-cell mRNA sequencing libraries and matching antigen-tracking libraries generated from the 10X Genomics system.
Web link https://github.com/rnabioco/antigen-tracking
 
Contributor(s) Hesselberth JR
Citation(s) 33843587
NIH grant(s)
Grant ID Grant title Affiliation Name
T32 AI007405 Training Program in Immunology UNIVERSITY OF COLORADO DENVER Raul Martin Torres
R35 GM119550 Coordination of RNA cleavage with end modification and processing UNIVERSITY OF COLORADO DENVER Jay R Hesselberth
R01 AI121209 Cooperation between lymphatic stroma and hematopoietic cells shapes protective immunity UNIVERSITY OF COLORADO DENVER Beth Ann Tamburini
Submission date May 17, 2020
Last update date Apr 13, 2021
Contact name Jay R. Hesselberth
E-mail(s) jay.hesselberth@cuanschutz.edu
Organization name University of Colorado School of Medicine
Department Biochemistry and Molecular Gentetics
Lab Jay Hesselberth
Street address 12801 E 17TH AVE
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (8)
GSM4732688 lymphnode_CD45neg_day2_mrna
GSM4732689 lymphnode_CD45neg_day2_antigen
GSM4732690 lymphnode_CD45pos_day2_mrna
Relations
BioProject PRJNA633370
SRA SRP262039

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
GSE150719_CD45neg_d14_barcodes.tsv.gz 33.2 Kb (ftp)(http) TSV
GSE150719_CD45neg_d14_features.tsv.gz 274.4 Kb (ftp)(http) TSV
GSE150719_CD45neg_d14_matrix.mtx.gz 44.3 Mb (ftp)(http) MTX
GSE150719_CD45neg_d2_barcodes.tsv.gz 6.0 Kb (ftp)(http) TSV
GSE150719_CD45neg_d2_features.tsv.gz 274.4 Kb (ftp)(http) TSV
GSE150719_CD45neg_d2_matrix.mtx.gz 10.1 Mb (ftp)(http) MTX
GSE150719_CD45pos_d14_barcodes.tsv.gz 25.8 Kb (ftp)(http) TSV
GSE150719_CD45pos_d14_features.tsv.gz 274.4 Kb (ftp)(http) TSV
GSE150719_CD45pos_d14_matrix.mtx.gz 34.5 Mb (ftp)(http) MTX
GSE150719_CD45pos_d2_barcodes.tsv.gz 41.7 Kb (ftp)(http) TSV
GSE150719_CD45pos_d2_features.tsv.gz 274.4 Kb (ftp)(http) TSV
GSE150719_CD45pos_d2_matrix.mtx.gz 56.7 Mb (ftp)(http) MTX
GSE150719_d14_DC_count_matrix.tsv.gz 9.5 Mb (ftp)(http) TSV
GSE150719_d14_DC_metadata.tsv.gz 292.3 Kb (ftp)(http) TSV
GSE150719_d14_FRC_count_matrix.tsv.gz 5.0 Mb (ftp)(http) TSV
GSE150719_d14_FRC_metadata.tsv.gz 147.0 Kb (ftp)(http) TSV
GSE150719_d14_LEC_count_matrix.tsv.gz 8.8 Mb (ftp)(http) TSV
GSE150719_d14_LEC_metadata.tsv.gz 275.3 Kb (ftp)(http) TSV
GSE150719_d2_DC_count_matrix.tsv.gz 15.6 Mb (ftp)(http) TSV
GSE150719_d2_DC_metadata.tsv.gz 494.5 Kb (ftp)(http) TSV
GSE150719_d2_FRC_count_matrix.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE150719_d2_FRC_metadata.tsv.gz 25.3 Kb (ftp)(http) TSV
GSE150719_d2_LEC_count_matrix.tsv.gz 1.5 Mb (ftp)(http) TSV
GSE150719_d2_LEC_metadata.tsv.gz 33.5 Kb (ftp)(http) TSV
GSE150719_walsh_d14_DC_metadata.tsv.gz 324.7 Kb (ftp)(http) TSV
GSE150719_walsh_d14_FRC_metadata.tsv.gz 163.8 Kb (ftp)(http) TSV
GSE150719_walsh_d14_LEC_metadata.tsv.gz 311.0 Kb (ftp)(http) TSV
GSE150719_walsh_d2_DC_metadata.tsv.gz 553.9 Kb (ftp)(http) TSV
GSE150719_walsh_d2_FRC_metadata.tsv.gz 28.2 Kb (ftp)(http) TSV
GSE150719_walsh_d2_LEC_metadata.tsv.gz 37.4 Kb (ftp)(http) TSV
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