Background:

This repo houses links to data for the SpaceTx Spacejam hackathons. If you have questions on the contents of the table below, please make an issue here. Updates on the SpaceTx wrapup and related publications will be announced here- stay tuned!

Spacetx SpaceJam 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!