MAPseq (Multiplexed Analysis of Projections by Sequencing) is a novel high-throughput method for brain mapping. It leverages next-generation sequencing to allow massive multiplexing of long-range projections, from thousands of cells, at single neuron resolution, from a single brain. (Kebschull et al, 2016 “High-throughput mapping of single neuron projections by sequencing of barcoded RNA”).

BARseq (barcoded anatomy resolved by sequencing) is a high-throughput, multiplexed method based on RNA barcoding that helps bridge anatomical and transcriptomic approaches at cellular resolution with the potential to discover organizing principles of neural circuits. (Chen et al, 2019 “High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing”)

Core Facility Staff

Resource Head

Anthony Zador, M.D., Ph.D.


Huiqing/Ching Zhan, Ph.D.

Other Core Staff

Renae Galluccio galluccio@cshl.edu
John Hover hover@cshl.edu
Diana Ravens dravens@cshl.edu
Yi-Chen Wu yicwu@cshl.edu
Jingyang Cai jcai@cshl.edu

MAPseq can be used to:

  • Quantify the projections of thousands—or even millions—of individual neurons in parallel within a single brain.
  • Produce multiple projection patterns from one to several injection sites, at single-neuron resolution.
  • Determine the brain-wide projections from a given area.
  • Compare projection patterns originating from different areas of the brain.
  • Determine whether individual neurons from a given area project to a specific area of interest.
  • Perform single-neuron tracing in less common animal model systems, including rodents and potentially non-human primates.

BARseq can be used to:

  • Sequence cellular barcodes in intact brain slices, preserve anatomical information and examine connectivity at greater resolution.
  • Map multiple measures in the same neurons: the connections, neuron activity via calcium imaging, and gene-expression data.
  • Expand the brain map by accurately pinpointing the location of a neuron.
  • Be potentially used for barcode-assisted lineage tracing, and map long-range axonal projections.
  • Be used for genetic labeling.

This core provides reagents and protocols for single neuron labeling, and helps users in processing tissue samples for high throughput sequencing. Services include:


  • Sindbis virus barcode library preparation: Providing Sindbis virus library containing millions of barcodes.
  • Sample processing for MApseq: RNA extraction, Reverse Transcription and PCR to make the library for Next Generation Sequencing.
  • Next Generation Sequencing for MApseq: Submitting the library to CSHL Next Generation Sequencing Core Facility for PE36 NextSeq run.
  • Preliminary sequencing data analysis for MAPseq: Analyzing the Next Generation Sequencing raw data and generating Barcode Marix (the abundance of each barcoded neuron in each tissue sample).


  • Provides reagents and protocols for single neuron labeling.
  • Probe design: help user design padlocks for genes of interest, or provide users with gene probe sets pre-designed to specific circuits of interest.
  • Consultations and training: discuss the parameters of the proposed project, clarify the experimental design and limitations, and help users apply BARseq to their research.


Please contact core director Ching Zhan at hzhan@cshl.edu for estimated costs.

Orders can be placed through the iLab Solutions MapSeq core.

NIH neurological disorders and stroke logo

MAPseq/BARseq Core facility is supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under Award Number U24NS126938.