/data

data for spacejam2

Primary LanguageJupyter Notebook

data!

Method species N datasets gene list spot table cell x gene notes
1 DARTFISH M. musculus and H. sapiens DARTFISH_genes SpotTable Human 1 (frontal cortex) SpotTable Human 2 (occipital cortex), SpotTable Mouse 1 CellxGene Human (frontal cortex) 1, CellxGene Human 2 (occipital cortex) CellxGene Mouse 1 stitched DAPI for Mouse dataset
2 MERFISH (Zhuang: MOp) M. musculus MERFISH_genes
3 osmFISH M. musculus osmFISH_inhibitory_genes (mouse VISp), osmFISH_excitatory_genes (mouse VISp) New and Improved Data: excitatory New and Improved Data: inhibitory needs segmentation! DAPI_excitatory_roi1_0-125_126-219,PolyT_excitatory_roi1_0-125_126-219
4 BARISTASeq M. musculus BARISTASeq_genes SpotTable Mouse VISp CellxGene Mouse VISp layer annotations
5 ISS M. musculus and H. sapiens ISS_genes SpotTable Human 1 MTG(FOVs 540) SpotTable Mouse 1 VISp (FOVs 704) SpotTable Human MTG 2 (FOVs 460) SpotTable Mouse VISp 2 (FOVs 140) SpotTable Mouse VISp 3 (FOVs 143) SpotTable Human MTG 3 (FOVs 378) SpotTable Human MTG 4 (FOVs 621) cellxgene Human MTG 1 (FOVs 540) cellxgene Mouse VISp 1 (FOVs 704) cellxgene Human MTG 2 (FOVs 460) cellxgene Mouse VISp 2 (FOVs 140) cellxgene Mouse VISp 3 (FOVs 143) cellxgene Human MTG 3 (FOVs 378) cellxgene Human MTG 4 (FOVs 621) Viktors genexcell. * DAPI Human 1 (FOVs 540) DAPI Mouse 1 (FOVs 704) DAPI Human 2 (FOVs 460) DAPI Mouse 2 (FOVs 140) DAPI Mouse 3 (FOVs 143) DAPI Human 3 (FOVs 378) DAPI Human 4 (FOVs 621)
6 ExSeq M. musculus ExSeq spot table CellxGene Table mouse
7 SeqFISH M. musculus SeqFISH SeqFISH spot table SeqFISH cell x gene (Cai lab) note: gene names in all lowercase (e.g. "sst", "gad1") are non-barcoded and have clearer spatial structure.
8 MERFISH (Allen: VISp, same panel as Zhuang lab above) M. musculus MERFISH_genes SpotTable Mouse VISp with anatomy CellxGene Mouse VISp stitched DAPI MIP
9 Allen smFISH VISp, (spacejam1) M. musculus smfish_genes SpotTable Mouse VISp nucleus segmentation (geojson)
10 10x-Visium/ST M. musculus n/a n/a observation x gene table 1, observation x gene table 2, observation x gene table 3, observation x gene table 4 each file is a gzipped tsv Example analysis
11 Slide-seq have lots of data, need help wrangling!

old data!

THIS SPREADSHEET contains links to all the data and many of the analyses from the first spacejam, including the RNA-seq reference data and consensus clusters. Several of these files are shared in the "spacetx" slack workspace. Please ask Jeremy to invite you if needed, or if you have any questions about data access for things in this table.

results!

Please post your results HERE!

Add a row to the relevant sheet corresponding either to the data-set or meta-analysis that you have done or add additional sheets as needed. Make sure the link to your result is here as well as a separate link (if needed) to some details about what your result actually means so others can use your results or compare their results against yours.