|
| Status |
Public on Feb 28, 2019 |
| Title |
Infected_KO |
| Sample type |
SRA |
| |
|
| Source name |
Liver of WT:Tbx21-/- mixed bone marrow chimera
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cells genotype: CD45.2+ Tbx21-/-
tissue: Liver
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
WT:Tbx21-/- mixed bone marrow chimeras were generated by combining CD45.1+ WT bone marrow cells with CD45.2+ Tbx21-/- bone marrow cells in a 1:1 ratio and transplanting mixture of cells into a lethally irradiated CD45.1+ WT recipient. 8 weeks later, some mice were infected with 200 tachyzoites of the Prugniaud strain of T. gondii. Thirty-five days post infection, liver lymphocytes were isolated. CD3– CD19– NK1.1+ NKp46+ that were either CD45.1+ or CD45.2+ were separately FACS sorted
Droplet-based 3′ end massively parallel single-cell RNA sequencing (scRNAseq) was performed by encapsulating sorted live CD45+ tumor infiltrating cells into droplets and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v1 according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using an Illumina HiSeq2500. 14x98nt read lengths were used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sorted CD45.2+ CD3– CD19– NK1.1+ NKp46+ cells from livers of T. gondii-infected WT:Tbx21-/- mixed bone marrow chimeras
|
| Data processing |
quality control, Cell Ranger Single Cell Software Suite (v1.3.1)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v1.3.1)
barcode processing, Cell Ranger Single Cell Software Suite (v1.3.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v1.3.1)
alignment, Cell Ranger Single Cell Software Suite (v1.3.1)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.
|
| |
|
| Submission date |
Jan 02, 2019 |
| Last update date |
Feb 28, 2019 |
| Contact name |
Maxim N. Artyomov |
| E-mail(s) |
martyomov@pathology.wustl.edu
|
| Organization name |
Washington University in St.Louis
|
| Department |
Immunology&Pathology
|
| Street address |
660 S. Euclid Avenue, Campus Box 8118
|
| City |
St.Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE124577 |
Toxoplasma gondii Infection Promotes NK Cell Conversion into ILC1s and Heterogeneous ILC1 Populations |
|
| Relations |
| BioSample |
SAMN10686108 |
| SRA |
SRX5195159 |
