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Series GSE261034 Query DataSets for GSE261034
Status Public on Jun 05, 2024
Title Single-cell transcriptomic analysis of mouse lung cDC2s at various times post allergic sensitization
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary Conventionaldendritic cells (cDCs) in the lung that drive effector T cell differentiation, and initiate allergic responses upon inhalation of allergens. CD11b+type 2 cDCs (cDC2s) are heterogeneous, but the relationship among subpopulations has been elusive. To analyze their developmental pathways of cDC2 subpopulations, we performed single cell RNA-sequencing (scRNAS-Seq) of total lung cDC2s at various times following inhalation of house dust extracts, and detected multiple clusters based on their differential transcriptomes. The data of cDC2 transcriptome at steady state, early and later stages after activation will be applicable for the maturation pathway analysis of cDC2s.
 
Overall design CD11b+cDC2s (CD45+ CD11c+ I-A+ Siglec-F– CD88– F4/80– CD103– Live/Dead–) from naive C57BL/6 mice, and mice 6 and 18 hours after inhalation house dust extract together with ovalbumin werepurified by flow cytometry sorting, and labeled with barcoded antibodies then loaded into the Single Cell Chip followed by forming single cell. The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v3 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library) andsequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read 1: 28; Read 2: 90).
 
Contributor(s) Cook DN, Nakano H
Citation(s) 38883724
Submission date Mar 06, 2024
Last update date Jun 28, 2024
Contact name Hideki Nakano
E-mail(s) nakanoh@niehs.nih.gov
Phone 984-287-4227
Organization name NIEHS
Department Immunity, Inflammation and Disease Laboratory
Lab Immunogenetics
Street address 111 TW Alexander Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (6)
GSM8132846 Lung-DC-0h-ADT
GSM8132847 Lung-DC-6h-ADT
GSM8132848 Lung-DC-18h-ADT
Relations
BioProject PRJNA1084858

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
GSE261034_Lung-DC.barcode_annotation.txt.gz 88.1 Kb (ftp)(http) TXT
GSE261034_RAW.tar 35.5 Mb (http)(custom) TAR (of TXT)
GSE261034_Samples_ADT_barcodesequences.txt.gz 179 b (ftp)(http) TXT
GSE261034_features.txt.gz 221.8 Kb (ftp)(http) TXT
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