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Series GSE216236 Query DataSets for GSE216236
Status Public on Oct 25, 2022
Title Gene expression and VDJ TCR profile of follicular T cells from immunized with nuclear proteins and control mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Analysis of follicular helper and follicular regulatory T cell subsets suggests that acquasition of nuclear proteins by antigen-specififc B cells promotes an increase in follicular regulatory T cells with immunosupressive gene expression profile
Overall design Four C57BL/6J mice were subcutaneously immunized with SA-DEL (streptavidin linked to biotinylated Duck Egg Lysozyme) in Ribi adjuvant. At 8 d.p.i. two mice were boosted with SA-NucPrs (streptavidin linked to biotinylated nuclear proteins, including bovine nucleosomes, Jo-1, Scl-70, Ro, SmRNP) in Ribi and two mice boosted with SA in Ribi for control. Follicular T cells (CD4+PD1hiCXCR5hi) were sorted from draining lymph nodes of mice at day 11 after immunization into PBS + 2% FBS. Single cell suspensions were subjected to counting and viability checks on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 700 -1000 cells/ul. Single cell libraries were generated using the 10x Genomics Chromium Controller with Immune Profiling reagents following the manufacturer’s protocol (10x Genomics). Final library quality was assessed using the LabChip GX (PerkinElmer). Libraries were subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10x Genomics) was used to align reads and generate count matrices. Barcodes with mitochondrial reads > 5% were removed. Preprocessing, clustering, and dimensionality reduction were performed using Loupe Browser and Loupe V(D)J browser (10x genomics, Cell Ranger). Graph-based clustering of Tfrs were visualized in 2D using UMAP algorithm.
Contributor(s) Grigorova IL, Ke F
Citation(s) 36862132
Submission date Oct 20, 2022
Last update date Jun 14, 2023
Contact name Irina Grigorova
Organization name University of Michigan
Department Microbiology and Immunology
Street address 1150 W MEDICAL CENTER DR
City Ann Arbor
ZIP/Postal code 48109
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (8)
GSM6663294 SA-1_GEX
GSM6663295 SA-1_VDJ
GSM6663296 SA-2_GEX
BioProject PRJNA892631

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Supplementary file Size Download File type/resource
GSE216236_DemuxStats_5077-FK.csv.gz 587 b (ftp)(http) CSV
GSE216236_RAW.tar 159.8 Mb (http)(custom) TAR (of CSV, TAR)
GSE216236_metrics_summary.csv.gz 938 b (ftp)(http) CSV
GSE216236_web_summary.html.gz 1.3 Mb (ftp)(http) HTML
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Raw data are available in SRA
Processed data provided as supplementary file

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