Supplementary Figure 1: Subcellular fractions are enriched for distinct protein and RNA markers.
From: RNA structure maps across mammalian cellular compartments
a, Widefield imaging of intact mES cells (left), mES nuclei after cytosol extraction, but excluding nonidet P-40 (NP-40) detergent in buffer (middle, control), and mES nuclei after cytosol extraction and ER removal (right). Nuclear (DAPI) stain shown in blue, and ER tracker dye in red. b, Western blots of protein markers for different subcellular compartments for HEK293 cells. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for the cytoplasmic fraction (cy), small nuclear ribonucleoprotein U1 subunit 70 (SNRP70) for the nucleoplasmic fraction (np), and histone H3 for the chromatin fraction (ch). Protein from the whole cell (wc) is shown for comparison. c, RT-qPCR of RNA markers of different cellular compartments. For GAPDH and U1, the RT (reverse transcription) primers target spliced (mature) mRNAs, whereas for ACTIN mRNA, an intron is targeted. d-e, Western blots of protein markers for mES cells with (d) DMSO treatment and (e) NAI-N3 treatment. ACTIN for the cytoplasmic and nucleoplasmic fractions (cy and np), small nuclear ribonucleoprotein U1 subunit 70 (SNRP70) for the nucleoplasmic fraction (np), and histone H3 for the chromatin fraction (ch).
