SpaceTx Data¶

Downloadable Datasets¶

Method	Info	Data Links
BARISTASeq	BARISTASeq_Readme.txt	cell_by_gene.csv mapped_cell_table.csv spot_table.csv
Multiplexed smFISH	smFISH_Readme.txt	cell_by_gene.csv mapped_cell_table.csv spot_table.csv
ExSeq	ExSeq_Readme.txt	cell_by_gene.csv mapped_cell_table.csv spot_table.csv
MERFISH (Allen Institute prototype)	MERFISH_Allen_Prototype_Readme.txt	cell_by_gene.csv mapped_cell_table.csv spot_table.csv
ISS	ISS_Readme.txt	cell_by_gene.csv mapped_cell_table.csv spot_table.csv

Experimental Methods¶

Method	Multiplexed smFISH	Allen MERFISH	hybridization-based in situ sequencing	ExSeq	Visium	BaristaSeq
Readout mechanism	non-barcoded	barcoded	sequencing-based	sequencing-based	spatial barcoding, sequencing en mass	sequencing-based
Enzymatic Amplification	no	no	yes	yes	no readout imaging	yes
Publications	https://www.ncbi.nlm.nih.gov/pubmed/30392798, https://www.nature.com/articles/s41467-021-23807-4	This unpublished MERFISH data is from a prototype pipeline with max projected z-stacks prior to decoding.	https://academic.oup.com/nar/article/48/19/e112/5912821#282922333	https://doi.org/10.1126/science.aax2656	https://science.sciencemag.org/content/353/6294/78 https://www.10xgenomics.com/products/spatial-gene-expression/	https://doi.org/10.1093/nar/gkx1206
Number of genes	22	254	human: 120, mouse: 119	mouse: 42	Full transcriptome	76
Area Imaged	~3mm²	~1.9mm²	human: 26.6mm², mouse: 53.6mm²	mouse: ~1mm²	6.5mm²	0.75 x 1.2 mm
Tissue Thickness	10 μm	10 μm	10 μm	20 μm	10 μm
Detection Sensitivity (high: same order of magnitude as smFISH, medium: ~1 OoM lowerthan smFISH, low: more than 1 OoM counts per cell below smFISH)	high	medium	low	medium	n/a	low
Average Total Counts Per Cell	225	919	human: 38.6, mouse: 30	mouse: 177 (for cells passing QC)	n/a	70
Cellular Spatial Resolution?	yes	yes	yes	subcellular	no	yes
Reagent Cost Per Experiment (USD)		500		500
Time Per Experiment	1 week	24 hours imaging, 4 days sample prep after sectioning	< 1 week	4 days (imaging); 1 week of sample prep prior	~1 day

In addition to the image-based spatial transcriptomics methods above, we also analyzed data from a sequencing-based method:

Visium: Visium is a (commercial) sequencing-based technique, where spatially barcoded oligonucleotides with a poly-T sequence are used to capture mRNA from fresh frozen tissue samples. In the Visium platform, capture locations (hereafter; spots), containing the barcoded oligonucleotides, are arranged according by “orange-crate packing” forming an equidistant hexagonal grid. Spots have a center to center distance of 100μm and a diameter of 55μm. A square region with sides of 6.5mm, containing 4992 spots, constitute the capture area onto which tissue samples are attached. Brightfield images are taken of the tissue samples after staining with hematoxylin and eosin (HE-images). Count data, obtained after sequencing, can be computationally aligned to the HE-images and related to morphological features.