Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses

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 nucleotide (nt) in length and upwards, from over 200, 000 individual human induce d 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.
Subject Area
- Biochemistry (7346)
- Bioengineering (5321)
- Bioinformatics (20259)
- Biophysics (10013)
- Cancer Biology (7742)
- Cell Biology (11298)
- Clinical Trials (138)
- Developmental Biology (6437)
- Ecology (9950)
- Epidemiology (2065)
- Evolutionary Biology (13318)
- Genetics (9360)
- Genomics (12581)
- Immunology (7700)
- Microbiology (19016)
- Molecular Biology (7439)
- Neuroscience (41029)
- Paleontology (300)
- Pathology (1229)
- Pharmacology and Toxicology (2135)
- Physiology (3157)
- Plant Biology (6860)
- Synthetic Biology (1895)
- Systems Biology (5311)
- Zoology (1089)