Figure 4.

Megakaryocyte-associated proteins and pathway classification of transcripts and proteins decreased in level following ZNF648 knockdown. Total RNA and whole cell protein lysates were prepared from erythroid cells differentiated from adult peripheral blood (PB) CD34+ cells transduced with scrambled (Scr) or ZNF648 short hairpin RNA (shRNA), at day 8 in culture. RNA was used to screen human genome arrays, with transcripts decreased in level by ≥2-fold following ZNF648 knockdown (KD) entered into Reactome. Data from three independent KD experiments (A). Tryptic peptides were prepared from cell lysates and labeled with Tandem Mass Tags followed by nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC MS/MS) with (B) relative decrease in level of megakaryocyte associated proteins following ZNF648 KD, identified amongst the 123 unique proteins decreased by ≥2-fold. Data from two independent KD experiments ± standard deviation, and (C) Reactome analysis of the proteins decreased in level. In (A) and (C) dark shades indicate genes/proteins apportioned to the pathway shown on the left. Pathways shown with minimum probability of over representation in the dataset, corrected for false discovery rate of P<0.006 for transcripts and P<1.42x10-5 for proteins.