DOI: 10.5061/dryad.sbcc2frm6
title: Bulk RNA sequencing analysis of Lin- leukemia BCR-ABL and BCR-ABL/MSI2-HOXA9 cells (post-transplantation)

description: 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 &lt;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).
description: 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.
description: # Bulk RNA sequencing analysis of Lin- leukemia BCR-ABL and
 BCR-ABL/MSI2-HOXA9 cells (post-transplantation) Dataset DOI:
 [10.5061/dryad.sbcc2frm6](https://doi.org/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