Dataset Open Access

Integrated spatial genomics dataset

Yodai Takei; Long Cai

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.

Files (46.1 GB)
Name Size
DNAseqFISH+.zip
md5:c4e7b23df669bbc7ef9b1436712b4a2c
144.0 MB Download
IF-binned1x1x1-E14-replicate1-Pos0.zip
md5:113ef6da421bccee05b13036f13e9c13
3.3 GB Download
IF-binned1x1x1-E14-replicate1-Pos1.zip
md5:2aeb9f7947d91e9253f9c0c6c9b1cdeb
2.7 GB Download
IF-binned1x1x1-E14-replicate1-Pos2.zip
md5:498435237b40618278bd30838e7ba1fc
3.6 GB Download
IF-binned1x1x1-E14-replicate1-Pos3.zip
md5:31f6f6849af65114b219e19102507fc8
3.2 GB Download
IF-binned1x1x1-E14-replicate1-Pos4.zip
md5:21e25a076802e8a89ce5dace95f5c6ce
2.5 GB Download
IF-binned1x1x1-E14-replicate2-Pos0.zip
md5:b9c43e770349dec28e2e49296e593f7f
2.0 GB Download
IF-binned1x1x1-E14-replicate2-Pos1.zip
md5:577b3b0b94cf2eb18ad1f625114c2848
2.5 GB Download
IF-binned1x1x1-E14-replicate2-Pos2.zip
md5:11806a92fbe06fb75a5afab6354f2e6b
1.8 GB Download
IF-binned1x1x1-E14-replicate2-Pos3.zip
md5:cffeae196d7f0957d5760d6e4deac9e3
2.8 GB Download
IF-binned1x1x1-E14-replicate2-Pos4.zip
md5:b2553697dfd0c9647f00ff432c92cc21
2.0 GB Download
IF-binned1x1x1-E14-replicate2-Pos5.zip
md5:e86f6358fcb723fe26c91af9ce4cea8c
2.2 GB Download
IF-binned2x2x1-E14-1kintron.zip
md5:4c305f8a55ba2dd187dcaa21fe97488b
2.2 GB Download
IF-binned2x2x1-E14-clonal24hr-Ch1.zip
md5:62aa6f978e75d33687adf7c011a16087
4.8 GB Download
IF-binned2x2x1-E14-clonal24hr-Ch2.zip
md5:7a0b535a852ca2622cfff76534b4b9cb
4.6 GB Download
IF-binned2x2x1-E14-clonal24hr-Ch4.zip
md5:e8b770593784516eee567256b3faea50
266.1 MB Download
IF-binned2x2x1-E14-clonal48hr.zip
md5:ccee78e29b101127564df79ef31cd366
5.6 GB Download
IF_supp_table_hyb_targets.xlsx
md5:4d703672f6143fd337db5254f429f72e
17.1 kB Download
RNAseqFISH.zip
md5:06e41028c1baeba7a2c6e4f8f8835708
1.0 MB Download
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