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 |
...working on it... |
| 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! |