MERFISH Data and Protocols
MERFISH is an imaging method capable of simultaneously measuring the copy number and spatial distribution of hundreds to thousands of RNA species in single cells. This technique was introduced in the paper:
We have introduced a revised set of MERFISH protocols that allow the number of measured cells to be increased substantially. These methods are described here:
We recently introduced a sample clearing approach customized for smFISH and MERFISH. This approach and the performance enhancements it provides are described here:
Additional Data and Resources
A Methods in Enzymology paper describing in greater detail the protocols necessary to perform a MERFISH experiment.
Example MERFISH Data 1
A set of example raw MERFISH data, analyzed data, and various files useful in the analysis of MERFISH data. The barcode sets that were used for the 14-bit MHD2 and 16-bit MHD4 codes are also included.
Example MERFISH Data 2
A set of files used to demonstrate the use of the fast and efficient probe design pipeline introduced in:
MERFISH Analysis Software
All of the MERFISH software is now available on github, including example scripts that utilize the example data above.
All identified RNA molecules in the 140-gene measurements
This excel table contains properties of all identified RNA molecules in the 140-gene experiments using the 16-bit MHD4 code.
is a unique index assigned to independent experiments on different days.
specifies the version of the two shuffled 16-bit MHD4 codebook used.
represents a unique index assigned to each imaged cell in each experiment.
is an integer representation of the binary barcode observed for that RNA.
is the name of the assigned gene.
is 1 only if the word is an exact match to an RNA code word.
is 1 only if the word is a corrected match with one-bit error originally.
represent the position of the cell within the sample measured in microns.
represent the centroid position of the each RNA spot measured in nanometers.