|
| Status |
Public on Mar 25, 2024 |
| Title |
CP CML T cells 6 |
| 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 |
49428_T_WT-CML_1352-854
|
| 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 |
Le Xuan Truong Nguyen |
| Organization name |
City of Hope
|
| Department |
Hematology/Bone Marrow T MC
|
| Street address |
1218 S 5TH AVE
|
| City |
Monrovia |
| State/province |
CA |
| ZIP/Postal code |
91016 |
| 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 |
SAMN40526527 |
| SRA |
SRX23977713 |
