bioRxivCell BiologyPreprint
Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses
Eswar P. R. Iyer, Sukanya PunthambakeriD, Songlei LiuiD, Kunal Jindal, Michael Farrell, Jernej Murn, Thomas Ferrante, Stewart Rudnicki, Richie E. KohmaniD, Asmamaw T. Wassie, Daniel GoodwiniD, Fei CheniD, Shahar AloniD, Anubhav SinhaiD, Denitsa MilanovaiD, Liviu Aron, Conor Camplisson, Alex Skrynnyk, Paul Louis Reginato, Nick Conway, John AachiD, Bruce Yankner, Edward S. BoydeniD, George M. ChurchiD
Abstract
We present Barcoded Oligonucleotides Ligated On RNA Amplified for Multiplexed and parallel In-Situ analysis (BOLORAMIS), a reverse-transcription (RT)-free method for spatially-resolved, targeted, in-situ RNA identification of single or multiple targets. For this proof of concept, we have profiled 154 distinct coding and small non-coding transcripts ranging in sizes 18 nucleotides in length and upwards, from over 200, 000 individual human induced pluripotent stem cells (iPSC) and demonstrated compatibility with multiplexed detection, enabled by fluorescent in-situ sequencing. We use BOLORAMIS data to identify differences in spatial localization and cell-to-cell expression heterogeneity. Our results demonstrate BOLORAMIS to be a generalizable toolset for targeted, in-situ detection of coding and small non-coding RNA for single or multiplexed applications.
- organism: human
- assay: spatial transcriptomics
- research focus: cell type annotation
- research focus: differential expression
- research focus: spatial domain detection
- approach: experimental assay
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