Title: Human monocytes exposed to conditioned medium of OCI-Ly3 cell line

The OCI-Ly3 cell line was maintained in RPMI1640 supplemented with 2mg/ml
glutamine and 10% fetal calf serum. For the production of lymphoma conditioned
media, cells were seeded at a density of 5 x 10^5 cells/ml and incubated in
complete RPMI 1640 medium for two days. Cell supernatants were centrifuged at
300 g for 10 minutes at 4 degree C.

PBMCs of healthy donors were isolated from fresh buffy coats by
density-gradient centrifugation over Biocoll Separating Solution (Biochrom,
Berlin, Germany). CD14+ monocytes were obtained from PBMCs by magnetic cell
separation using CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany)
according to the manufacturer’s instructions. Purity of CD14+ cells after
magnetic cell separation was determined by staining with specific markers and
quantification by flow cytometry using a FACSCanto II (BD Biosciences).
Monocytes were differentiated in the presence of lymphoma-conditioned medium
mixed in equal parts with complete RPMI1640.
Total RNA was isolated from monocytes that had differentiated into macrophages
using the NucleoSpin Kit (Machery-Nagel).
Sequencing libraries were generated from polyadenylated RNA and sequenced at
GATC (Konstanz, Germany) on an Illumina HiSeq instrument with a read length of 50 nt.
Sequences are provided in fastq format. Qualities are Sanger-encoded. The
fastq file was compressed with bzip2.