Supplementary processed data. The raw microscopy data are not uploaded owing to their large size (2.9 Tb), but are available upon reasonable request (Long Cai: lcai@caltech.edu). These supplementary processed data contain additional files for RNA seqFISH, DNA seqFISH+ and sequential immunofluorescence. DNAseqFISH+.zip contains DNA seqFISH+ pixel locations for 3,600 loci in single cells (pixel sizes are 103 nm for x and y, and 250 nm for z). Please refer to Supplementary Table 1 at the journal website for genomic coordinates of the targeted loci. RNA seqFISH.zip contains RNA seqFISH expression profiles for mRNAs and introns in single cells. Intron data also contain pixel coordinates for intron spot locations. Cells were filtered out if keep1 column is 0 due to the laser illumination bias. Excel file contains additional information for sequential immunofluorescence experiments. The file contains target names with corresponding hybridization cycle round and fluorescent channel information per each experiment. Zip files for IF binned data contain IF intensity information in each pixel coordinate (either bin1 or bin2). Please refer to the included excel file to match each target to each hybridization and fluorescent channel.