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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 10, 2023 |
| Title |
Trypanosome-infected mice, bone marrow, scRNA-seq |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow cells
tissue: Bone marrow
strain: C57BL/6
age: 6-8 weeks old
infection: Trypanosome-infected
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow cells were collected from CO2 euthanized mice by isolating and flushing femurs, using a 26-gauge needle and 1 mL ice-cold DMEM (Capricorn Scientific, Ebsdorfergrund, Germany) supplemented with 1% FBS (Atlas Biologicals, CO, USA) and 1% penicillin/streptomycin (Capricorn Scientific, Ebsdorfergrund, Germany. Cell suspensions were centrifuged at 314 x g at 4oC for 7 mins. Cell pellets were re-suspended in 3 mL FACSFlow Sheath Fluid (BD Biosciences, CA, USA) containing 0.05% FBS (Atlas Biologicals, CO, USA) and total remaining live cells were counted using Trypan Blue (Sigma-Aldrich, Missouri, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, bone marrow cells 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 reversetranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. These 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 P5 and P7 primers 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 conducted using the Cell Ranger software v7.0.1 (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 |
Jun 02, 2023 |
| Last update date |
Aug 10, 2023 |
| Contact name |
Magdalena Radwanska |
| E-mail(s) |
magdalena.radwanska@ghent.ac.kr
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| Organization name |
Ghent University Global Campus
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| Street address |
119-5, Songdomunhwa-ro
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| City |
Incheon |
| ZIP/Postal code |
21985 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE234000 |
Single-cell transcriptome profiling of mouse bone marrow-derived immune cells in response to trypanosome infection |
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| Relations |
| BioSample |
SAMN35573996 |
| SRA |
SRX20581237 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7440363_Trypanosome-infected_filtered_barcodes.tsv.gz |
33.9 Kb |
(ftp)(http) |
TSV |
| GSM7440363_Trypanosome-infected_filtered_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM7440363_Trypanosome-infected_filtered_matrix.mtx.gz |
57.3 Mb |
(ftp)(http) |
MTX |
| GSM7440363_Trypanosome-infected_raw_barcodes.tsv.gz |
3.2 Mb |
(ftp)(http) |
TSV |
| GSM7440363_Trypanosome-infected_raw_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM7440363_Trypanosome-infected_raw_matrix.mtx.gz |
72.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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