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Sample GSM8037212 Query DataSets for GSM8037212
Status Public on Jan 31, 2024
Title scRNA-seq of KO-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 Li Du
Organization name City of Hope
Department Toni Stephenson Lymphoma Center
Lab KCRB 1028
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 SAMN39617491
SRA SRX23398977

Supplementary file Size Download File type/resource
GSM8037212_KO-CML-PB_processed_data.tar.gz 45.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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