SpaceTx Data

Downloadable Datasets

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This unpublished MERFISH data is from a prototype pipeline with max projected z-stacks prior to decoding.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.