Transcriptome characterization by RNA sequencing (The CLL project)

The Chronic Lymphocytic Leukemia (CLL) Genome Project ( aims to generate a comprehensive catalogue of genomic alterations involved in the development and progression of the disease. This information will improve our ability to diagnose and categorize the patients and will promote the advance in new therapeutic approaches.

Researchers at the Centre for Genomic Regulation have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. The transcriptome of 219 CLL patients, including 95 of the RNA-seq samples, was also analyzed using DNA microarrays. We have complemented the analysis with exome-sequencing previously performed in 76 of the 98 cases and microarray methylation data that match 85 CLL RNA-seq samples. We have monitored with unprecedented resolution the CLL transcriptome. Our work has revealed new insights into the molecular pathogenesis of CLL, and has lead to the discovery of new molecular subtypes of this disease with potential clinical implications.

An open-access paper describing this work has been recently published in Genome Research:

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Below you can find the paper’s supplementary table:

1  RNA-seq read statistics (.xls format);

2)   Differential Gene Expression (.xls format);

3)   Differential Splicing (.xls format);

4)   Item Consensus Clustering (.xls format);

5)   Chimeric Junctions (.xls format);

Gene and Transcript quantifications for the RNA-seq data:

a)    gene RPKM table  (gz compressed file)

b)   transcript RPKM table (gz compressed file)

c)    gene read counts table (gz compressed file)

Sequencing and expression array data have been deposited at the European Genome-Phenome Archive (EGA,, which is hosted at the European Bioinformatics Institute (EBI), under accession number EGAS00001000374.

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