|
| Status |
Public on Jan 31, 2024 |
| Title |
scRNA-seq of WT-CML-PBMC |
| Sample type |
SRA |
| |
|
| Source name |
PBMC from Mir142+/+ BCR-ABL mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: PB
cell type: PBMC
genotype: Mir142+/+BCR-ABL
|
| Treatment protocol |
The cells were not treated.
|
| Growth protocol |
The cells were collected from the mice and sorted by flow cytometry before performing scRNA-seq. The cells have not been cultured or growed in vitro.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were captured on a 10xGenomics Chromium Controller using a 10X V3 Single Cell 3’ Solution kit (10xGenomics, Chromium Single Cell 3’ Reagent kit V3, Cat. PN-1000092). All protocols were performed following the manufacturer’s instructions.
Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat. 5067-4626). The library concentration was determined with a Qubit High Sensitivity DNA Assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired-end setting of 28 cycles of read (R) 1, 101 cycles of R2, and 8 cycles of index reads on Illumina NovaSeq 6000 platform, with sequencing depth of ~0.1 million reads per cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v5.0.0
Counting data of reference gene expression levels were generated by cellranger v5.0.0 (automatic identification of chemistry properties)
Assembly: mm10
Supplementary files format and content: Tab separated values; MatrixMarket
|
| |
|
| Submission date |
Jan 26, 2024 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Wenyong Chen |
| Organization name |
City of Hope
|
| Department |
Cancer Biology
|
| Street address |
1500 E. Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE254285 |
T cell Immune Escape in Blast Crisis Transformation of Chronic Myeloid Leukemia |
| GSE261822 |
Investigating Immune Escape of Chronic Myeloid Leukemia in Blast Crisis by Comparing T cells from miR-142 KO BCR-ABL versus miR-142 WT BCR-ABL mice |
|
| Relations |
| BioSample |
SAMN39617494 |
| SRA |
SRX23398974 |
