Mar 12, 2026
MAPseq and BARseq Dual Sectioning Event for a Single Mouse Brain
- Allen Institute1
- 1Allen Institute for Brain Science
- Allen Institute for Brain ScienceTech. support
Protocol Citation: Allen Institute 2026. MAPseq and BARseq Dual Sectioning Event for a Single Mouse Brain. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4p18rlo5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 12, 2026
Last Modified: March 16, 2026
Protocol Integer ID: 313189
Keywords: MAPseq/BARseq, planar sectioning, sequencing projection barcode, frozen brain tissue, unique barcode sequence, barseq dual sectioning event, fresh brain tissue, sindbis virus barcode library, axonal projections of individual neuron, single mouse brain, injections of sindbis virus barcode library, projection barcode, barcode, mapseq experiment, cells by gene expression, individual neuron, rna, gene expression, transduced cell, tissue processing, axonal projection, gene, brain, subsequent processing for in situ
Abstract
This protocol enables tissue processing for combined BARseq- MAPseq experiments where axonal projections of individual neurons transduced by unique barcode sequences can be mapped across the brain, with concurrent molecular characterization of transduced cells by gene expression. Mice receive injections of Sindbis virus barcode library targeting region of interest, and fresh brain tissue will be harvested and frozen in OCT 24 hours later. Frozen brain tissue will be stored at -80°C to preserve RNA until ready for sectioning and subsequent processing for in situ sequencing of genes and barcodes and next generation sequencing projection barcodes in dissected tissue.
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