Chemo-naïve CLL patient protocol

Peripheral blood from chemo-naïve CLL patients participating in a previously reported clinical trial (AGMT-REVLIRIT trial, ClinicalTrials.gov Identifier: NCT00738829 and NCT01703364) [18 (link)] with first line treatment with lenalidomide in combination with fludarabine and rituximab was collected upon informed consent and ethical approval by the Ethics Committee of the Province of Salzburg (415-E/1287/4–2011, 415-E/1287/8–2011). Sampling was performed prior treatment start and CLL cells were obtained by density gradient centrifugation and B-CLL Cell Isolation kit (Miltenyi Biotec). Cell purity was >90% in all samples. The determination of prognostic markers was performed routinely at our department as described previously [19 (link)]. DNA and RNA was purified using DNeasy Blood and Tissue kit or RNeasy Mini kit (both Qiagen), respectively. Patient details and type of analysis are given in supporting Table 1. Primers are listed in supporting Table S2. RNA/DNA sequencing data from AGMT-REVLIRIT patients and MEC1 cells are available under BioProject PRJNA540189 at https://www.ncbi.nlm.nih.gov/sra. In addition, RNA sequencing and clinical data from CLL samples and normal B cells were downloaded from the European Genome-phenome Archive (EGAS00001000374) [20 (link)].