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Sample GSM8412807 Query DataSets for GSM8412807
Status Public on Jan 22, 2025
Title EP/pSpike, scRNA-seq-BCR (Spleen)
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: BALB/c
age: 6–8 weeks old
tissue: Spleen
treatment: Mice were intramuscularly immunized with EP/pSpike using ICHOR medical systems. Each group was immunized three times biweekly with a dose of DNA 40 μg/mouse.
cell type: CD45+ cells
Treatment protocol For preventive spike vaccine immunization, mice were intramuscularly immunized with LNP-M/Ctrl, LNP-M/Spike-mRNA, EP/pSpike, and LNP-M/pSpike. Each group was immunized three times biweekly with a dose of 40 μg/mouse for DNA or 5 μg/mouse for mRNA. For a syngeneic mouse colon cancer model, a single-dose treatment of LNP-M/Ctrl or LNP-M/pR282W-mAb (40 μg/mouse) was administered intratumorally on day 14 post-tumor inoculation.
Growth protocol For preventive spike vaccine immunization, BALB/c mice were grown to 6-8 weeks old, immunization was administered.. For a syngeneic mouse colon cancer model, C57BL/6 mice were inoculated with MC38-p53KO/R282W cells (5 × 105 cells/mouse) subcutaneously. When the tumors were palpable (~100 mm3), treatment was administered.
Extracted molecule total RNA
Extraction protocol The single-cell suspension of spleens from mice immunized 3 times vaccine was prepared, and CD45+ cells were purified using the EasySep™ Mouse TIL (CD45) Positive Selection Kit following the manufacturer’s instructions. Tumors were harvested 14 days following LNP-pR282W-mAb or LNP-Ctrl treatment, single cell suspensions were prepared. The cells of spleen or tumor samples were resuspended in RPMI1640 with 5% FBS. To create the scRNA-seq libraries, equivalent numbers of single cells from three mice per group were combined at a density of 1 × 103 cells/μl in a 10% FBS RPMI1640 medium. Each group used about 10,000 cells, which were converted to barcoded scRNA-seq libraries using the ChromiumTM Next GEM Single Cell 5′ Kit v2 (10× Genomics, Pleasanton, CA, USA; 1000263) according to the manufacturer’s protocol. To prepare full-length T-cell Receptor (TCR) and B-cell Receptor (BCR)V(D)J libraries, Chromium Single Cell Mouse TCR Amplification Kit (10× Genomics, 1000254) and Chromium Single Cell Mouse BCR Amplification Kit (10× Genomics, 1000255) was used to enrich amplified cDNA from the 5′ libraries.
Approximately 10,000 cells were allocated for the 10× Genomics 5′ v2 single-cell assay. TCR/BCR libraries were prepared using the Chromium™ single cell V(D)J enrichment kit (10× Genomics). Reverse transcription, cDNA amplification and library preparation were executed following the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10× Genomics
Data processing The CellRanger Count v7.1.0 pipeline (https://cloud.10xgenomics.com) was used to process the raw sequence data in FASTQ format. The data were aligned to the mouse reference genome, using default barcode assignment and Unique Molecular Identifier (UMI) counting, with a 2020-A version of the mouse (mm10) genome reference. line used the default parameters with the mouse GRCm38/mm10 reference genome.
Assembly: mm10
Supplementary files format and content: gz
 
Submission date Jul 22, 2024
Last update date Jan 22, 2025
Contact name Dafei Chai
E-mail(s) chaidafei8@gmail.com
Organization name Baylor College of Medicine
Street address Alkek Building One Baylor Plaza
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL24247
Series (1)
GSE272803 Lipid nanoparticles deliver DNA-encoded biologics and induce potent protective immunity
Relations
BioSample SAMN42742112
SRA SRX25414730

Supplementary file Size Download File type/resource
GSM8412807_EP_pSpike_BCR_S3_filtered_contig_annotations.csv.gz 1.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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