|
Status |
Public on Jan 31, 2024 |
Title |
scRNA-seq of WT-CML-SPLEEN-T cells |
Sample type |
SRA |
|
|
Source name |
Spleen-T from Mir142+/+ BCR-ABL mice
|
Organism |
Mus musculus |
Characteristics |
tissue: Spleen cell type: T cells 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
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|
|
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 |
SAMN39617492 |
SRA |
SRX23398976 |