Supplementary files for integrated spatial genomics in mouse brain cortex

Supplementary raw and processed data. The raw microscopy data are not uploaded owing to their large size (2.6 Tb), but are available upon reasonable request (Long Cai: lcai@caltech.edu).

These supplementary data contain additional files for RNA seqFISH, DNA seqFISH+ and sequential immunofluorescence from three biological replicates in mouse brain cortex. Voxel sizes are 103 nm for x and y, and 250 nm for z. Please refer to Table S1 at the journal website for genomic coordinates of the DNA seqFISH+ loci.

Table S5 (provided as a CSV file): RNA seqFISH expression profiles for mRNAs and introns in single cells.

Table S6 (provided as a CSV file): Voxel coordinates for intron spot locations in single cells.

Table S7 (provided as a CSV file): DNA seqFISH+ spot voxel locations for 1-Mb resolution data in single cells. (finalcellID: final cell ID 1-2,762; replicateID: 1-3; rep: original replicate number (2-4); fov: FOV ID in each biological replicate; cellID: original cell ID (including doublets) in each FOV and each biological replicate; cluster label: transcriptionally defined cluster (1-9); channel: fluorescent channel; geneID: locus name; chromID: 1-20 (Chr1-19, ChrX); x: x voxel coordinate; y: y voxel coordinate; z: z voxel coordinate; labelID: DBSCAN cluster ID (ID 0 or larger are clustered loci and ID -1 is non-clustered loci); XistID for ChrX (0 for active X, 1 for inactive X based on Xist chromatin states))

Table S8 (provided as a CSV file): DNA seqFISH+ spot voxel locations for 25-kb resolution data in single cells. Same column annotation as Table S7.

Table S9 (provided as a CSV file): Chromatin profiles (fraction of loci within 300 nm from immunofluorescence marker exterior) for each immunofluorescence marker and each cell type for 2,460 genomic loci with 1-Mb resolution.

Table S10 (provided as a CSV file): Median radial positioning score (from 0 to 1; 0: nuclear center; 1: nuclear periphery) for 2,460 genomic loci with 1-Mb resolution for each cell type. 

Additional Zip folders for subnuclear marker (IF, DAPI, ncRNA) raw intensity information in each voxel coordinate for each cell. Files are named with position (FOV ID) and cellID for each FOV (original cellID including doublets, please refer to Table S4 to obtain finalcellID with 2,762 cells used for the analysis).