{"id":"CU21355","slug":"rna-and-atac-mutual-sequencing--CU21355","source":{"id":"CU21355","dataset":"techtransfer","title":"RNA and ATAC mutual sequencing (RAM-seq) for simultaneous single-cell transcriptome and chromatin profiling","description_":"<p>This technology is a multiplex single-cell sequencing workflow that simultaneously profiles RNA expression and chromatin accessibility at high depth within individual cells. </p>\r \r<h2>Unmet Need: Affordable, instrument free joint single-cell RNA and chromatin profiling</h2>\r \r<p>Single-cell multi-omics is essential for resolving cellular heterogeneity and the regulatory mechanisms behind disease and therapeutic response. Existing workflows that simultaneously measure transcriptome and chromatin accessibility depend on dedicated microfluidic instruments that are costly to acquire and operate. Furthermore, existing methods use inefficient chemistry that produces poor-quality reads, much of which is thrown out during quality checks, pushing up the cost per cell. These barriers limit access for smaller research groups and constrain the scale at which biopharma can run discovery campaigns. </p>\r \r<h2>The Technology: Plate-based dual RNA/ATAC profiling</h2>\r \r<p>This technology is a single-cell sequencing workflow that simultaneously profiles RNA expression and chromatin accessibility (ATAC) sequencing without dedicated microfluidic instruments. Single cells are sorted into individual microwell plate wells, where both RNA transcripts and tagmented chromatin fragments are captured using a commercially available template-switching reverse transcriptase and tagged with well-specific barcodes. Pooled libraries are then amplified and sequenced using standard sequencing platforms, with the scalability down to as few as 96 cells per run. By eliminating the need for specialized third-party library preparation instruments and enabling processing directly in a microwell plate, this approach simplifies workflow and improves retention of 90% of cells passing quality control filtering. This platform is also compatible with ERCC spikes-ins and downstream analytical pipelines, without requiring chemical or physical partitioning prior to amplification. </p>\r \r<h2>Applications:</h2>\r \r<ul>\r<li><p>Joint single-cell transcriptome and chromatin accessibility profiling  </p></li>\r<li><p>Multiplexed single-cell analysis of transcriptome, chromatin accessibility, and cell-surface markers </p></li>\r<li><p>Characterization of therapeutic mechanism of action </p></li>\r<li><p>Standalone single-cell RNA-seq or ATAC-seq library generation </p></li>\r</ul>\r \r<h2>Advantages:</h2>\r \r<ul>\r<li><p>Eliminates the need for dedicated microfluidic single-cell instrumentation </p></li>\r<li><p>Reduces per-cell sequencing cost relative to ligation-based workflows </p></li>\r<li><p>Improves read quality through template-switching reverse transcription </p></li>\r<li><p>Compatible with major sequencing platforms </p></li>\r<li><p>Integrates with existing plate-based laboratory equipment and reagents </p></li>\r</ul>\r \r<h2>Lead Inventor:</h2>\r \r<p><a href=\"https://zuckermaninstitute.columbia.edu/tom-maniatis-phd\">Thomas Maniatis, Ph.D.</a> </p>\r \r<h2>Patent Information:</h2>\r \r<p>Patent Pending (<a href=\"https://patents.google.com/patent/US20240093183A1/en?oq=US+18%2f339%2c789\">US 20240093183</a>) </p>\r \r<h2>Related Publications:</h2>\r \r<ul>\r<li><a href=\"https://pubmed.ncbi.nlm.nih.gov/41687613/\">Kandror EK, Carriere M, Peterson A, Liao W, Tjärnberg A, Fung JH, Mahbubani KT, Loper J, Pangburn W, Xu Y, Saeb-Parsy K, Maniatis T, Rizvi AH. “Enhancer dynamics and cellular architecture in the human spinal cord” Neuron. 2026 Apr 15;114(8):1399-1418.</a> </li>\r</ul>\r \r<h2>Tech Ventures Reference:</h2>\r \r<ul>\r<li>Licensing Contact: <a href=\"mailto:techtransfer@columbia.edu\">Joan Martinez</a>  </li>\r</ul>","tags":["Chemical library","Chromatin","Microfluidics","Multiplexing","Neuron","RNA-Seq","Reverse transcriptase","Scalability","Spinal cord","Transcriptome","Workflow"],"file_number":"CU21355","collections":[],"meta_description":"RAM-seq enables simultaneous single-cell RNA and chromatin profiling without microfluidics, using plate-based dual-omics sequencing.","apriori_judge_output":"{\"scores\":{\"novelty\":4.0,\"potential_impact\":4.0,\"readiness\":3.0,\"scalability\":3.0,\"timeliness\":4.0},\"weighted_score\":3.5,\"risks\":[\"Potential IP/patent landscape uncertainty (patent-pending) may affect freedom-to-operate.\",\"Requires validation across multiple cell types to confirm robustness beyond initial platform compatibility.\"],\"one_sentence_take\":\"RAM-seq is a promising multi-omics single-cell approach with solid novelty and impact, reasonable readiness, and good timeliness, but IP status and cross-cell-type validation remain key risk factors.\"}","inventors":["Abbas Rizvi Ph.D.","Elena Kandror","Thomas P. Maniatis Ph.D."],"manager":"Joan Martinez","depts":["Biochemistry & Molecular Biophysics","Mortimer B. Zuckerman Mind Brain Behavior Institute"],"divs":["Columbia University Medical Center (CUMC)"],"date_released":"2026-08-27"},"highlight":{},"matched_queries":null,"score":0.0}