|
| Status |
Public on Jul 24, 2024 |
| Title |
Floxed control TIM-3 KO sample #1 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell line: WEHI-3B
cell type: T cells
genotype: Havcr2fl/fl
treatment: TBI + BM/Tc transplantation
|
| Treatment protocol |
Mice received lethal total body irradiation and subsequent AML cells (10 000 cells) and bone marrow transplantation (5.106 BM cells). On day 2, mice were injected with 200 000 donor T cells isolated from the spleen of donor mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were isolated on day 23 post BMT, and cells were smashed through a 75 µm cell strainer to obtain cell suspension. T cells were then isolated using pan-T cell isolation kit (Miltenyi). T cells were finally stained with H2K-b (donor haplotype) antibody (Biolegend, reference 116603) labelled with an oligotag (TotalSeq™-B0952, Biolegend, reference 405287), allowing scRNA-seq analysis of selected engrafted donor T cells. Cells were handled according to 10xGenomics Cell preparation guidelines though the whole process.
Samples were processed using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index – 10x Genomics) and 3’ Feature Barcoding (10X genomis, 16 rxns PN-1000262) following manufactures protocol. In short: GEM´s were generated using a Chromium Controller (10x Genomics) at a target cell recovery rate of 10.000. GEM-RT and subsequent clean-up was performed. cDNA was amplified and 3’ Gene Expression Dual Index Library Construction was performed. Illumina paired-end, dual indexing was performed. For all amplification steps a Veriti 96 Well Thermal Cycler (appledbiosystems) and for all quality control steps a 2200 TapeStation (Agilent Technologies) was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired fastq files were processed with cellRanger (6.1.2) with the transcriptome index from Mouse mm10 (2020-A) downloaded from 10xgenomics website.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Sep 05, 2023 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Geoffroy Andrieux |
| Organization name |
University clinics Freiburg
|
| Street address |
Breisacherstr 153
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE242334 |
Targeting oncogene-dependent TIM-3 induces T cell reprogramming thereby enhancing graft-versus-leukemia immunity - scRNAseq |
|
| Relations |
| BioSample |
SAMN37286291 |
| SRA |
SRX21638618 |
