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| Status |
Public on Apr 24, 2024 |
| Title |
GCB_Cre_Pos, scRNA-seq |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: GC B cells
genotype: Cre+
treatment: tamoxifen
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| Treatment protocol |
CD4CreERt2 x IL21 fl/fl (Cre negative used as littermate controls) mice were treated with 4 mg Tamoxifen on days 16, 17, and 18 post-infection with Plasmodium yoelii.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Splenic germinal center B cells were enriched using anti-GL-7-PE and anti-PE microbeads (Miltenyi Biotec), then FACS-sorted (BD FACSAria II) CD19+B220+CD95+GL-7+ cells from day 32 P. yoelii-infected Cre neg (IL21fl/fl, pooled from n = 4) littermate control or CD4CreERT2 x IL21fl/fl (IL21Δ/Δ, pooled from n = 4) mice that were treated with Tamoxifen on days 16-18 p.i. Sorted cells were loaded onto the 10x Chromium X Controller (10x Genomics) with a target cell number of 10,000 cells per sample.
scRNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (dual index) (10x Genomics) according to the manufacturer’s protocols. Barcoded libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument (IIHG, University of Iowa) using a NovaSeq SP v1.5 Reagent Kit (138 total cycles) (Illumina) with the following cycle counts: 28 (read 1), 10 (i7 Index), 10 (i5 Index), 90 (read 2). Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
scRNA-seq
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1, 10x Genomics Cloud Analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jan 16, 2024 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Noah S Butler |
| E-mail(s) |
noah-butler@uiowa.edu
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| Organization name |
University of Iowa
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| Department |
Department of Microbiology and Immunology
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| Lab |
Butler Lab
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| Street address |
4-350 BSB, 51 Newton Road
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| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE253397 |
scRNA-seq of day 32 p.i. GC B cells induced by experimental Plasmodium infection following the inducible deletion of IL-21 from CD4 T cells on day 16-18 |
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| Relations |
| BioSample |
SAMN39463793 |
| SRA |
SRX23254805 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8020030_GCB_cre_pos_barcodes.tsv.gz |
36.3 Kb |
(ftp)(http) |
TSV |
| GSM8020030_GCB_cre_pos_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM8020030_GCB_cre_pos_matrix.mtx.gz |
56.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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