|
Status |
Public on Jan 15, 2024 |
Title |
Sample1_D7_Transcriptome |
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.
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|
|
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.
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|
|
Submission date |
Mar 14, 2023 |
Last update date |
Jan 15, 2024 |
Contact name |
Xin Gao |
E-mail(s) |
xin.gao@anu.edu.au
|
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 |
|
Relations |
BioSample |
SAMN33761287 |
SRA |
SRX19678070 |