|
| Status |
Public on Aug 28, 2023 |
| Title |
Day 2 Parasites_Astrocyte, scRNA seq |
| Sample type |
SRA |
| |
|
| Source name |
Purified from primary murine astrocytes
|
| Organism |
Toxoplasma gondii |
| Characteristics |
cell line: Purified from primary murine astrocytes
cell type: parasite
genotype: ME49EW Strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Toxoplasma tissue cysts were purified from brain homogenate using a percoll density gradient. Tissue cysts were treated with pepsin-HCl mixture to excyst bradyzoites; Parasites that were cultured in human foreskin fibroblast or primary murine astrocytes were needle passed and run through a 3 μm filter on indicated timepoint. All parasites were used for scRNA seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, parasites 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. 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: ME49 Toxoplasma Reference Genome
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Aug 07, 2022 |
| Last update date |
Aug 28, 2023 |
| Contact name |
Edward Vizcarra |
| E-mail(s) |
[email protected]
|
| Phone |
8409991854
|
| Organization name |
UC Riverside
|
| Street address |
26985 Gold Dust Court
|
| City |
Corona |
| State/province |
California |
| ZIP/Postal code |
92883 |
| Country |
USA |
| |
|
| Platform ID |
GPL26742 |
| Series (1) |
| GSE210671 |
An ex vivo model of Toxoplasma recrudescence reveals the developmental plasticity of the bradyzoite stage |
|
| Relations |
| BioSample |
SAMN30181531 |
| SRA |
SRX16965375 |
