MAPseq/BARseq

Overview of Services

MAPseq (Multiplexed Analysis of Projections by Sequencing) is a novel high-throughput method for brain mapping. MAPseq 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”).

BARseq (Barcoded Anatomy Resolved by Sequencing) is a high-throughput, multiplexed method that bridge anatomical and transcriptomic approaches at cellular resolution by in situ sequencing. BARseq uses in situ sequencing to map neuronal projections and correlates neuronal projections to gene expression with high throughput and low cost.

The services in the MAPseq/BARseq core facility include: Sindbis virus barcode library preparation, sample processing for MAPseq(including RNA extraction, and library preparation for sequencing), next generation sequencing, and preliminary data analysis for MApseq. The Core facility also provides consultations and training for BARseq.

Leadership

Core Head

Anthony Zador, Professor
zador@cshl.edu

Core Director

Ching Zhan, Research Assistant Professor
hzhan@cshl.edu

Location and hours of operation

Hours	Location
Monday-Friday 9:00 am - 5:00 pm	Woodbury Genome Research Center Room#167.1 500 Sunnyside Boulevard Woodbury, NY 11797

Getting Started

**For Cold Spring Harbor Laboratory individuals: First-time users should click "Register" in upper right. Returning users will click "Sign In".

**For Non-CSHL individuals: After you register, you must be assigned an Activity Number before service request.

Please contact the center manager for further information.

Contacts

Name	Role	Phone	Email	Location
Ching/Huiqing Zhan	Core Director	516-367-5083	hzhan@cshl.edu	Woodbury genome research center Room#167.1

In House Services Price List

Name	Description	Price
Cryostat sectioning for manual dissection	This service provides 200-300 um cryostat sections for manual dissection purpose from fresh frozen tissue. Extra care is taken during cryostat sectioning to avoid cross sample contamination. The sections are stored at -80oC before dissection.	Inquire
High Output NextSeq, 400M of reads	Sequencing the MAPseq library by PE36 NextSeq *Price per library	Inquire
MapSeq library preparation-- per 24 samples	RNA extraction, QC for RNA quality and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing.	Inquire
MapSeq library preparation-- per 96-well plate	RNA extraction, QC for RNA quality and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing.	Inquire
MapSeq library preparation--per 12 samples	RNA extraction, QC for RNA and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing.	Inquire
MAPseq library preparation--per 48 samples	RNA extraction, QC for RNA and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing	Inquire
Preliminary sequencing data processing	We offer a preliminary Next Generation Sequencing (NGS) data processing service that includes the analysis of raw data and the generation of a Barcode Matrix, which provides information on the abundance of each barcoded neuron in each tissue sample. Our pricing is based on a per sequencing run basis. Starting from June 1st, 2023, our data processing service will undergo a significant update, resulting in a remarkable drop in the cost of data processing. Our new and improved pipeline is designed to be more efficient and faster, allowing us to deliver high-quality results at a much more competitive price point. This update represents our commitment to providing exceptional value to our users.	Inquire
Sindbis virus barcode library expressing GFP	Provide Sindbis virus library containing millions of barcodes. The estimated barcode diversity of current batch of virus is ~20M. The titer of the virus is ~2x10^9 infectious particles/ml *price per 24 aliquot-- 4ul/aliquot	Inquire
Sindbis virus barcode library expressing mRuby	Provide Sindbis virus library containing millions of barcodes. The estimated barcode diversity of current batch of virus is ~19M. The titer of the virus is ~2x10^11 infectious particles/ml *price per 24 aliquot-- 4ul/aliquot	Inquire
Test virus order	This test virus has the same vector sequence as the barcoded virus library, but it contains only one barcode. This virus could be used for practicing Sindbis virus injection. Each order contains 4 aliquots of virus (4ul/aliquot), which should be enough for at least 8 injections.	Inquire

Search available services: View: by category alphabetically

Name	Description	Price
▼ ► Cryostat Sectioning and Tissue Dissection (1)
Cryostat sectioning for manual dissection	This service provides 200-300 um cryostat sections for manual dissection purpose from fresh frozen tissue. Extra care is taken during cryostat sectioning to avoid cross sample contamination. The sections are stored at -80oC before dissection.	Inquire
▼ ► Data analysis (1)
Name	Description	Price
Preliminary sequencing data processing	We offer a preliminary Next Generation Sequencing (NGS) data processing service that includes the analysis of raw data and the generation of a Barcode Matrix, which provides information on the abundance of each barcoded neuron in each tissue sample. Our pricing is based on a per sequencing run basis. Starting from June 1st, 2023, our data processing service will undergo a significant update, resulting in a remarkable drop in the cost of data processing. Our new and improved pipeline is designed to be more efficient and faster, allowing us to deliver high-quality results at a much more competitive price point. This update represents our commitment to providing exceptional value to our users.	Inquire
▼ ► Next Generation Sequencing (1)
Name	Description	Price
High Output NextSeq, 400M of reads	Sequencing the MAPseq library by PE36 NextSeq *Price per library	Inquire
▼ ► Sample Processing (4)
Name	Description	Price
MapSeq library preparation-- per 24 samples	RNA extraction, QC for RNA quality and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing.	Inquire
MapSeq library preparation-- per 96-well plate	RNA extraction, QC for RNA quality and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing.	Inquire
MapSeq library preparation--per 12 samples	RNA extraction, QC for RNA and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing.	Inquire
MAPseq library preparation--per 48 samples	RNA extraction, QC for RNA and injection quality (bioanalyzer and q-PCR), Reverse Transcription and PCR to make the library for next generation sequencing	Inquire
▼ ► Virus (3)
Name	Description	Price
Sindbis virus barcode library expressing GFP	Provide Sindbis virus library containing millions of barcodes. The estimated barcode diversity of current batch of virus is ~20M. The titer of the virus is ~2x10^9 infectious particles/ml *price per 24 aliquot-- 4ul/aliquot	Inquire
Sindbis virus barcode library expressing mRuby	Provide Sindbis virus library containing millions of barcodes. The estimated barcode diversity of current batch of virus is ~19M. The titer of the virus is ~2x10^11 infectious particles/ml *price per 24 aliquot-- 4ul/aliquot	Inquire
Test virus order	This test virus has the same vector sequence as the barcoded virus library, but it contains only one barcode. This virus could be used for practicing Sindbis virus injection. Each order contains 4 aliquots of virus (4ul/aliquot), which should be enough for at least 8 injections.	Inquire