Bulk RNA sequencing analysis of Lin- leukemia BCR-ABL and BCR-ABL/MSI2-HOXA9 cells (post-transplantation)
Data files
Oct 21, 2025 version files 4.46 MB
-
BCRABL_Msi2Hoxa9_.csv
1.86 MB
-
BCRABL_Msi2Hoxa9_.xlsx
2.60 MB
-
README.md
3.51 KB
Abstract
To understand how the MSI2-HOXA9 translocation triggers blast crisis CML (bcCML), we compared gene expression patterns in BCR-ABL and BCR-ABL/MSI2-HOXA9-driven disease. RNA-seq analysis was carried out on lineage negative cells from leukemia established with BCR-ABL alone or with a combination of BCR-ABL and MSI2-HOXA9. Network mapping of all differentially expressed genes (q-value <0.05) using non-redundant functional grouping revealed an enrichment of metabolic processes with oncogenic pathways and developmental programs. Programs that were dominantly upregulated by MSI2/HOXA9 were those involved in development, including Aldh1a1, Erbb3, and Kit, consistent with BCR-ABL/MSI2-HOXA9 driving a more undifferentiated disease, known oncogenes, including Frat1, Map7, and Fzd3, and components of the mitochondria including mt-Co2, mt-Atp8, and mt-Nd5. Among the genes most enriched in BCR-ABL/MSI2-HOXA9-driven bcCML were key components of the mitochondrial respiratory chain, including Complex I, Complex III, Complex IV, and the F0 subunit of ATP synthase (mt-Atp6 and mt-Atp8).
Dataset DOI: 10.5061/dryad.sbcc2frm6
Description of the data and file structure
To understand how the MSI2-HOXA9 translocation triggers bcCML, we compared gene expression patterns in BCR-ABL and BCR-ABL/MSI2-HOXA9-driven leukemia. To this end, RNA-seq analysis was carried out on lineage negative cells from leukemia established with BCR-ABL alone or the combination of BCR-ABL and MSI2-HOXA9.
Lin- leukemia cells were sorted from mice transplanted with BCR-ABL/Control or BCR-ABL/MSI2-HOXA9 transduced KLS cells. Total RNA was isolated using the RNAeasy Micro Plus kit (QIAGEN). RNA libraries were generated from 150ng of RNA using Illumina's TruSeq Stranded mRNA Sample PrepKit (Illumina). Libraries were pooled ands single end sequenced (1x75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina). Resultant fastq files were pseudoaligned into transcript-level summaries using Kallisto. Transcript level summaries were processed into gene-level summaries using Sleuth and differential expression analysis was performed using the Wald test.
Files and variables
File: BCRABL_Msi2Hoxa9_.csv
Description: The data depicts processed RNA-seq data composed gene names in the first column followed by TPM values of the corresponding genes in each condition (BCR-ABL or BCR-ABL/MSI2-HOXA9) in triplicate. The data was generated using the Kallisto/Sleuth pipeline.
The same data is also attached as an excel document (see below).
Variables
- Gene: Gene IDs; in some instances there are blank cells, which are missing values. These correspond to targets that do not have a corresponding NCBI gene name. Largely, these genes are not expressed (TPM~0).
- BA_LR: TPM values of the first replicate of BCR-ABL control condition
- BA_RP: TPM values of the second replicate of BCR-ABL control condition
- BA_RR: TPM values of the third replicate of BCR-ABL control condition
- BAMH_LL: TPM values of the first replicate of BCR-ABL/MSI2-HOXA9 condition
- BAMH_LP: TPM values of the second replicate of BCR-ABL/MSI2-HOXA9 condition
- BAMH_NOP: TPM values of the third replicate of BCR-ABL/MSI2-HOXA9 condition
File: BCRABL_Msi2Hoxa9_.xlsx
Description: The data depicts processed RNA-seq data composed gene names in the first column followed by TPM values of the corresponding genes in each condition (BCR-ABL or BCR-ABL/MSI2-HOXA9) in triplicate. The data was generated using the Kallisto/Sleuth pipeline.
The same data is also attached as a CSV file (see above).
Variables
- Gene: Gene IDs; in some instances there are blank cells, which are missing values. These correspond to targets that do not have a corresponding NCBI gene name. Largely, these genes are not expressed (TPM~0).
- BA_LR: TPM values of the first replicate of BCR-ABL control condition
- BA_RP: TPM values of the second replicate of BCR-ABL control condition
- BA_RR: TPM values of the third replicate of BCR-ABL control condition
- BAMH_LL: TPM values of the first replicate of BCR-ABL/MSI2-HOXA9 condition
- BAMH_LP: TPM values of the second replicate of BCR-ABL/MSI2-HOXA9 condition
- BAMH_NOP: TPM values of the third replicate of BCR-ABL/MSI2-HOXA9 condition
Code/software
The same data is uploaded and available in both Excel (.xlsx) and comma separated (.csv) formats.
Access information
N/A
Lin- leukemia cells were sorted from mice transplanted with BCR-ABL/Control or BCR-ABL/MSI2-HOXA9 transduced KLS cells. Total RNA was isolated using the RNAeasy Micro Plus kit (QIAGEN). RNA libraries were generated from 150ng of RNA using Illumina's TruSeq Stranded mRNA Sample PrepKit (Illumina). Libraries were pooled ands single end sequenced (1x75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina).
Resultant fastq files were pseudoaligned into transcript-level summaries using Kallisto. Transcript level summaries were processed into gene-level summaries using Sleuth and differential expression analysis was performed using the Wald test.