DOI: 10.1126/science.aaf2403

The following datasets have been published in Science (AAAS) under the title “Visualization and analysis of gene expression in tissue sections by spatial transcriptomics” on July 1, 2016.

For questions regarding the datasets, please contact:

Fredrik Salmén
Jose Fernandez

Sequencing and image files

Raw data (fastq) Hematoxylin & eosin stained brightfield image

ST pipeline and spatial barcode IDs

The ST datasets were generated using the ST Pipeline (v. 0.3.8), with genome and annotation files described in the publication. The ID files used to demultiplex the reads can be found here.

ID file 1000L2 was used for the MOB replicates 1-4.
ID file 1000L3 was used for the MOB replicate 5.
ID file 1000L5 was used for the rest of the MOB replicates.
ID file 1000L3 was used for the Breast Cancer replicates.

Count matrices

Gene counts for each ST spot are given here as count matrices, where gene names are columns and spot coordinates are rows. For all datasets, spots outside the tissue were removed. The coordinates of the spots were adjusted to account for variations during printing of the arrays.

count matrix compatible with the ST Viewer/R/Python etc.


If you want to plot the data on top of the HE image, you can either rescale the image to the array size (1,1,33,35) or transform the spot coordinates to image pixel coordinates using these alignment 3×3 matrices:

transformation matrix (to convert from array coordinates to image pixel coordinates) It can be used in the ST Viewer