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Sample GSM7099100 Query DataSets for GSM7099100
Status Public on Jan 15, 2024
Title Sample1_D7_Antibody_Capture
Sample type SRA
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: B cell (probe+ IgD- Ighg2A10)
treatment: Immunized with irradiated sporozoites
time point: D7
Extracted molecule total RNA
Extraction protocol 2x10^4 probe+ CD19+ Ighg2A10 B cells were transferred into recipient mice. 1-2 days later mice were immunized IV with 5x10^4 irradiated Pb-PfCSP sporozoites. At either 7 or 21 days post immunization mice were euthanized, spleens collected and probe+ IgD- Ighg2A10 B cells stained with TotalSeq-C feature and hashtag antibodies were isolated and sorted. Cells were then loaded into a Chromium (10x Genomics).
Indexed V(D)J, Feature Barcode and GEX libraries of sorted samples were prepared according to the protocol for Single Indexed 10X Genomics V(D)J 5' kit for mice with Feature barcoding kit (10X Genomics).Libraries were then sequenced using an Illumina NovaSeq6000.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10x Genomics
Data processing Cell Ranger (10X Genomics) was used to process the V(D)J, Feature Barcode and GEX sequences and prepare them for downstream analysis.
Seurat (version 3.1) (Butler et al., 2018) was used for graph-based clustering and visualizations of the gene expression data and demultiplexing.
The Immcantation portal were used to convert the 10X V(D)J output from CellRanger into an AIRR community standardized format to allow for further downstream analysis.
Assembly: mm10
Supplementary files format and content: Standard Cellranger output.
Submission date Mar 14, 2023
Last update date Jan 15, 2024
Contact name Xin Gao
Phone 0450031169
Organization name The Australian National University
Department Immunology
Street address 131 Garran Rd
City Canberra
State/province ACT
ZIP/Postal code 2601
Country Australia
Platform ID GPL24247
Series (2)
GSE227370 Lack of affinity signature for germinal center cells that have initiated plasma cell differentiation (Figure2)
GSE248377 Lack of affinity signature for germinal center cells that have initiated plasma cell differentiation
BioSample SAMN33761288
SRA SRX19678071

Supplementary file Size Download File type/resource
GSM7099100_Ab_Henry_1_Processed.tar.gz 40.1 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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