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. This method was first described by Anthony Zador’s team (Kebschull et al, 2016 “High-throughput mapping of single neuron projections by sequencing of barcoded RNA”).

Core Facility Staff

Resource Head

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

Research Investigator

Ching/Huiqing Zhan, Ph.D.

Core Technicians

Yan Li yali@cshl.edu
Nicole Gemmill gemmill@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 within one month.
  • 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.

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: RNA extraction, Reverse Transcription and PCR to make the library for Next Generation Sequencing.
  • Next Generation Sequencing: Submitting the library to CSHL Next Generation Sequencing Core Facility for PE36 NextSeq run.
  • Preliminary sequencing data analysis: Analyzing the Next Generation Sequencing raw data and generating Barcode Marix (the abundance of each barcoded neuron in each tissue sample).

Orders can be placed through the iLab Solutions MapSeq core


Rates last updated: Feb 2020

Service Unit External
Virus library – sufficient for 96 injections:
      ~20M barcodes (24 vials, 4 ul ea)
       Test virus with single barcodes (2 vials, 3ul ea)
per library   $1,570
Sample Processing 12 samples   $1,890
  24 samples   $3,360
  48 samples   $5,350
  96-well plate   $8,230
Sequencing (NextSeq high output PE36) per library   $2,360
Data analysis per library   $1,570
Total project (sample processing, sequencing, & analysis) 12 samples   $5,820
  24 samples   $7,290
  48 samples   $9,280
  96-well plate   $12,160