Data supporting the functional role of Eleven-nineteen Lysine-rich Leukemia 3 (ELL3) in B cell lymphoma cell line cells

The data presented here are related to the research article entitled “Selective expression of the transcription elongation factor ELL3 in B cells prior to ELL2 drives proliferation and survival” (Alexander et al., 2017) [1]. The cited research article characterizes Eleven-nineteen Lysine-rich Leukemia 3 (ELL3) expression in the B cell compartment and functional dependence in B lymphoma cell lines. This data report describes the mRNA expression pattern in a panel of cell lines representing the B cell compartment, supplementing the protein expression data presented in the associated research report. In addition, a reanalysis is presented of publicly available mRNA expression data from primary murine B cells to reveal dynamic regulation of the ELL family members post LPS stimulation (Barwick et al., 2016) [2]. The effect of ELL3 depletion on cell morphology, latent Epstein Barr Virus (EBV) lytic replication and differentiation markers in a Burkitt's lymphoma (BL) cell line cells are presented.


a b s t r a c t
The data presented here are related to the research article entitled "Selective expression of the transcription elongation factor ELL3 in B cells prior to ELL2 drives proliferation and survival" (Alexander et al., 2017) [1]. The cited research article characterizes Elevennineteen Lysine-rich Leukemia 3 (ELL3) expression in the B cell compartment and functional dependence in B lymphoma cell lines. This data report describes the mRNA expression pattern in a panel of cell lines representing the B cell compartment, supplementing the protein expression data presented in the associated research report. In addition, a reanalysis is presented of publicly available mRNA expression data from primary murine B cells to reveal dynamic regulation of the ELL family members post LPS stimulation (

Data
The mRNA levels of ELL, ELL2 and ELL3 in a B cell lymphoma cell line panel is depicted in Fig. 1A. Fig. 1B depicts the average mRNA per murine primary B cell following LPS stimulus and cell sorting based on cell division and plasma cell marker CD138 based on data from GSE70294 [2]. The effect of ELL3 depletion is shown in Fig. 2; including observations of cell morphological changes, PRDM1 mRNA expression, EBV lytic replication factors expression, B cell factors BCL6, PAX5, MYC, and immunoglobulin isoforms.

Cell culture
Cell lines and cell culture details are as described previously [1].

Quantitative mRNA analysis
RNA was extracted using the E.Z.N.A. Total RNA Kit I (Omega Bio-Tek, Norcross, GA) and reverse transcribed into cDNA with the qScript cDNA synthesis Kit (Quanta Biosciences Inc., Gaithersburg, MD). 3 µl of one to eleven diluted cDNA was analyzed in duplicate using primers specific to PRDM1α, EBV lytic replication genes (BZLF1, BMRF1 and BLLF1), and B cell and plasma cell factors (BCL6, PAX5, MYC, membrane-bound IgM, secreted IgM) at primer specific annealing temperatures. mRNA expression was analyzed using the ΔΔC t method, with 18 S as a normalization gene [4]. Primer sequences are described in Supplemental Table I and were designed to span exon-exon junctions and to amplify a single PCR product [3,[5][6][7][8][9]. The annealing temperatures were experimentally determined using a temperature gradient and high efficiency was validated by PCR of cDNA serial dilutions.

Microscopy
For time-lapse imaging, cells were plated on a 6-well flat bottom plate at 2×10 5 cells/ml, placed in Evos Onstage Incubator set at 37°C and 20%O 2 and imaged every 5 min for 24 h on Evos Auto FL Cell Imaging System (Thermo Fisher Scientific Inc., Waltham, MA). All images were taken at 20×magnification using the RFP filter and phase.