Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.
IF: 19.160
Cited by: 32


We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.


Gene Expression

MeSH terms

Cell Line
Gene Expression Profiling
In Situ Hybridization, Fluorescence
Single-Cell Analysis


Liu, Songlei
Punthambaker, Sukanya
Iyer, Eswar P R
Ferrante, Thomas
Goodwin, Daniel
Fürth, Daniel
Pawlowski, Andrew C
Jindal, Kunal
Tam, Jenny M
Mifflin, Lauren
Alon, Shahar
Sinha, Anubhav
Wassie, Asmamaw T
Chen, Fei
Cheng, Anne
Willocq, Valerie
Meyer, Katharina
Ling, King-Hwa
Camplisson, Conor K
Kohman, Richie E
Aach, John
Lee, Je Hyuk
Yankner, Bruce A
Boyden, Edward S
Church, George M

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