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Series GSE219259 Query DataSets for GSE219259
Status Public on Jan 16, 2024
Title Single-cell RNA-seq uncovers unique gene expression profiles in the spleen of hypoxic mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The stability of FOXP3 expression in Tregs influences the balance between tolerance and autoimmunity. Treg cell development and function are regulated by IL-2, which binds to IL-2Rα (also called CD25). Decreased expression of CD25 (Il2ra gene) characterizes Tregs that lose FOXP3 expression (exTregs) and undergo transdifferentiation into TH17 cells. This has been established under arthritic conditions but whether this Treg transdifferenciation into exTregs occur following hypoxia exposure, it is unknown. Therefore, single-cell RNA-seq (10x Genomics) was performed using a 10X Genomics Chromium system to test the hypothesis that hypothesis that chronic hypoxia initiates Treg transcriptional reprogramming.
Overall design We used mice (Foxp3EGFP-cre-ERT2, Ai14-tdTomato) in which tamoxifen administration uncoveres 4 populations of CD4+ T cells; EGFP+, EGFP+ tdTomato+, EGFP-tdtomato+, and EGFP-tdtomato-. We performed single-cell RNA sequencing (scRNA seq) in isolated splenocytes from tamoxifen-treated mice following 5 days of CH or normoxia; tdTomato (WPRE sequence) predominated in the CD4+ memory T cell cluster. Treg marker Il2ra (CD25) was used to identify the Treg cluster and comparative gene expression profiling analysis of RNA-seq data was performed for normoxic and CH samples.
Contributor(s) Bosc LG, Lantz BJ, Jones DT, Guo Y, Oyebamiji OM
Citation(s) 38347920
NIH grant(s)
Grant ID Grant title Affiliation Name
R56 HL153065 Novel collagen V-reactive natural Th17 cells in hypoxic pulmonary hypertension UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER Laura V Gonzalez Bosc
BioProject PRJNA904301
Submission date Dec 02, 2022
Last update date Feb 26, 2024
Contact name Laura Gonzalez Gonzalez Bosc
Organization name University of New Mexico Health Sciences Center
Department Cell Biology and Physiology
Lab LGBosc Lab
Street address Msc 084750, Brf 237J
City Albuquerque
State/province NM
ZIP/Postal code 87131-0001
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM6779279 FOXP3_GFP_Tom_WPRE_Sample1
GSM6779280 FOXP3_GFP_Tom_WPRE_Sample2
GSM6779281 FOXP3_GFP_Tom_WPRE_Sample3

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
GSE219259_Bosc_ProcessedData_AllCells.RData.gz 3.6 Gb (ftp)(http) RDATA
GSE219259_RAW.tar 406.9 Mb (http)(custom) TAR (of MTX, 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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