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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 10, 2023 |
| Title |
T. brucei 14dpi mouse spleen, scRNAseq |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
cell type: Whole splenocytes
tissue: Spleen
strain: C57BL/6
age: 6-8 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were prepared from freshly collected mouse spleensby homogenizing spleens in 4 mL of Dulbecco’s Modified Eagle Medium (DMEM) (Capricorn Scientific, Ebsdorfergrund, Germany) supplemented with 10% Fetal Bovine Serum (FBS) (Atlas Biologicals, CO, USA) and 1% penicillin/streptomycin (Capricorn Scientific, Ebsdorfergrund, Gemany), using gentleMACS™ Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany). After passing the homogenate through a 70 µm cell strainer (SPL Life Sciences, Gyeongi-do, Korea), cells were centrifuged at 314 x g at 4oC for 7 minutes. Cell pellets were resuspended in RBC lysis buffer (Biolegend, CA, USA) at 4oC and incubated for 5 minutes. Cells were washed and re-suspended in PBS supplemented with 0.04% BSA. Total remaining live cells were counted by Trypan Blue (Sigma-Aldrich, Missouri, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, splenocytes were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. were loaded into single cell chips (10X Genomics) and partitioned using Gel Bead In-Emulsion (GEM) technology and a Chromium Controller (10X Genomics). Single cell libraries were prepared using the 10X Genomics Chromium Single Cell 3`reagent kit v3. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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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 |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jan 12, 2023 |
| Last update date |
Aug 10, 2023 |
| Contact name |
Hien Thi Thu Pham |
| Organization name |
Ghent University Global Campus
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| Lab |
Biomedical Research Center
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| Street address |
Songdomunhwa-ro 119
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| City |
Incheon |
| ZIP/Postal code |
21985 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE222784 |
Neutrophil metalloproteinase driven spleen architecture breakdown hampers plasma cell generation and infection control of trypanosomiasis. |
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| Relations |
| BioSample |
SAMN32721113 |
| SRA |
SRX19024496 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6932273_14dpi_filtered_barcodes.tsv.gz |
52.6 Kb |
(ftp)(http) |
TSV |
| GSM6932273_14dpi_filtered_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM6932273_14dpi_filtered_matrix.mtx.gz |
75.5 Mb |
(ftp)(http) |
MTX |
| GSM6932273_14dpi_raw_barcodes.tsv.gz |
18.5 Mb |
(ftp)(http) |
TSV |
| GSM6932273_14dpi_raw_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM6932273_14dpi_raw_matrix.mtx.gz |
117.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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