Spatial Transcriptomics

MERFISH mouse dataset

spatial transcriptomics of mouse liver and kidney

About

The CZ Biohub MERFISH mouse dataset is a comparative study of MERFISH spatial transcriptomics in mouse liver and kidney with bulk and single-cell RNA sequencing data from Tabula Muris Senis. The work is in collaboration with Vizgen, Inc. and the University of California, San Francisco. See the bioRxiv preprint here.

Preprint

Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

In this web portal, you can access links to the raw data, processed data, and GitHub code repository. In addition, you can navigate to other pages in the portal to interactively look at some raw images and plots of MERFISH data.

Raw Data Available on AWS

Raw Data on AWS Open Datasets Registry

Raw MERFISH data is made available for anyone to use via Amazon S3

Processed data available from figshare

Processed Data

The gene panel codebook, RIN scores, and processed data including decoded MERFISH transcript information, cell boundaries, bulk RNA statistics, and single cell RNA counts with cell type annotations are available for download from figshare

Code Available on GitHub

GitHub repository

The GitHub repository containing the code to reproduce the figures in the main text of the manuscript can be found in github