GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE152387 Query DataSets for GSE152387
Status Public on Jun 13, 2020
Title Multiplexed single cell RNA/AbSeq sequencing of ex vivo Treg and ex-Treg from different time points
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: identify differentially expressed genes between ex-Treg obtained 5, 10 or 15 days post-adoptive transfer into a lymphopenic environment compared to ex vivo Treg in order to identify Treg subset with heightened instability.
Method: Treg from Foxp3YFP-Cre Rosa26RFP (PMID: 18387831, PMID: 17171761) were co-injected with congenically-disparated naive T cells in a 1:1 ratio into Rag1KO mice and ex-Treg were sorted at 15 days, 10 days or 5 days post-transfer. As a control, ex vivo Treg were sorted from Foxp3YFP-Cre Rosa26RFP (d0 sample). Next, samples were stained with multiplexing antibodies using the BD Single-Cell Multiplexing Kit (BD biosciences), then pooled and stained with the following oligonucleotide-conjugated antibodies: anti‑CD25 (PC61), anti-CD44 (IM7), anti-CD62L (MEL-14), anti-GITR (DTA-1), anti-CD4 (RM4-5), anti‑TCRb (H57-597), anti‑CD69 (H1.2F3), anti‑TIGIT (1G9), anti‑CD95 (Jo2), anti‑CD122 (TM‑1β), anti‑Tim-3 (5D12), anti‑CCR7 (4B12), anti‑CD103 (M290), anti‑CD279 (J43), anti‑CD274 (MIH5), anti‑CD233 (C9B7W), anti‑CD71 (C2), anti‑CD278 (7E7G9), anti‑ITGB7 (M293), anti‑CD137 (1AH2), anti‑CD40 (3/23), anti‑CD3e (145-2C) from BD Biosciences. Single-cell capture and cDNA library preparation was performed using the BD Rhapsody Single-cell analysis system (BD Biosciences), according to the manufacturer’s instructions, using a custom gene panel (591 genes). Sequencing was performed on an Illumina NextSeq500 instrument using a Mid‑Output kit v2.5 (150 cycles, paired-end). Sample demultiplexing, barcode processing, alignment, filtering, UMI counting were done using the standard BD Biosciences Rhapsody analysis pipeline on Seven Bridges (
Result: In this study, we showed that ex-Treg downregulate Treg core-specific genes immediatly upon adoptive transfer into a lymphopenic environment. Further, we identified a Treg population enriched for unstable Trg clones.
Conclusion: Our study was able to identify a Treg subset enriched for unstable Treg with plastic potential. This Treg subset appears highly enriched for naïve peripheral-induced Treg.
Overall design ex vivo Treg and ex-Treg 5, 10 or 15 days post-adoptive transfer into Rag1KO mice were sorted, stained for multiplexing antibodies and stained for Abseq antibodies. Cell capture and single cell RNA sequencing was performed for a custom gene panel using the BD Rhapsody and Illumina NextSeq500 instruments.
Contributor(s) Junius S, Lemaitre P, Mavrogiannis AV, Liston A, Schlenner SM, Kowalczyk E
Citation(s) 34301799
Submission date Jun 12, 2020
Last update date Aug 15, 2021
Contact name Susan M Schlenner
Organization name KU Leuven
Department Microbiology, Immunology and Transplantation
Lab Adaptive Immunity
Street address Herestraat 49
City Leuven
ZIP/Postal code 3000
Country Belgium
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (1)
GSM4614203 D0 Treg, D5/10/15 ex-Treg
BioProject PRJNA639149
SRA SRP267116

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
GSE152387_4_cell_types.txt.gz 314 b (ftp)(http) TXT
GSE152387_RAW.tar 7.0 Mb (http)(custom) TAR (of CSV, FASTA)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap