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Sample GSM8152164 Query DataSets for GSM8152164
Status Public on Mar 25, 2024
Title CP CML T cells 1
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: T cells
genotype: BCR-ABL
treatment: none
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA)
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's protocol.
RNA-seq libraries were sequencing on Illumina NovaSeq6000 with the sequencing length of 2x101bp. RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 49423_T_WT-CML_1352-862
Data processing RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Mar 18, 2024
Last update date Mar 25, 2024
Contact name Steven T Rosen
Organization name City of Hope
Department Department of Hematology and Hematopoietic Cell Transplantation
Street address 1500 E. Duarte Road
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL24247
Series (2)
GSE261798 Immune Escape of Chronic Myeloid Leukemia in Blast Crisis: The Cross-over of T cell microRNAs, Metabolism and Exhaustion
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 SAMN40526532
SRA SRX23977708

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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