Spatial and temporal gene expression

Spatially resolved, highly multiplexed RNA profiling in single cells

Figure 1

MERFISH = multiplexed error-robust FISH (fluorescence in situ hybridization), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells.

Each RNA labelled with set of encoding probes, which contain:

• targeting sequences that bind the RNA
• readout sequences that bind fluorescently labeled readout probes

Each RNA assigned a binary word in a modified, error-robust Hamming code:

• Sequences have $N$ bits, $N$ number of fluorescent labels
• Sequences have exactly four 1’s. Same number of ones guarantees same overall error rate in situation where $1\to 0$ and $0\to 1$ error rates are different.
• Sequences have a mutual Hamming distance of at least 4.

Hamming codes can do 1-bit error correction, see example on wikipedia. Higher calling rate and lower misidentification rate at the cost of encoding fewer RNA species with a given number of bits.

Figure 2