Click the links to download data files:

Batch corrected TPMs for treatment-naive samples (n=603)

log10(x+1) transformed before batch correction.
Covariates used for batch correction - see Methods in CLL-map manuscript for details.

Top 2500 most variable genes used for clustering in expression cluster discovery

 Raw TPMs for all CLLmap RNA-seqs (n=715)

Generated by RNA-SeQC v2.3.6 (GENCODE19)

Raw gene counts for all CLLmap RNA-seqs (n=715)

Generated by RNA-SeQC v2.3.6 (GENCODE19)

TSV file with all data used in i-comut plot
 JSON file with all data used in i-comut plot

Can be used for local icomut viewing using the icomut repo: https://github.com/broadinstitute/icomut-lattice

Mapping of Spanish ICGC sample IDs to CLL-map IDs

Notes:

1. See Clinical Data tab, which enables download of additional molecular and clinical data annotations.

2. Remove the following RNA-seq samples from the full (n=715) TPM and count files before analysis for a non-redundant cohort:
CRC-0007, CRC-0011, CRC-0028, CRC-0033, DFCI-5053, JB-0010
Consider also excluding GCLL-0136, which is suspected to be an MCL
See the CLL-map publication Supplementary Table 1 for details and for the set of samples included in each analysis.