Service Description

10X Genomics Single Cell 3’ RNA-seq

Cell populations are heterogeneous and unsynchronized in their characteris-

tics. Traditional bulk RNA sequencing generates comprehensive information

but does not provide insight into variable expression between cells. 10X

Genomics Chromium Single Cell 3′RNA-seq provides a scalable solution for

cell characterization and gene expression profiling of hundreds to millions of

cells. This technology is able to handle a large quantity of single cells fast and

accurately, providing research solutions across a wide variety of applications

including cancer, neurology, and immunology.

Sequencing Service Specification

BGI’s Single cell sequencing services are executed with our DNBseq technol-

ogy platform or Illumina platform:

• Sample preparation including tissue dissociation and dead

cell removal

• Single cell partition and amplification

• DNBseq PE100 or Illumina PE150 options

• Raw data and bioinformatics analysis are available in

standard file formats

Sample Preparation and Services

DNBseqTM is BGI’s proprietary sequencing technology, developed by our

Complete Genomics subsidiary in Silicon Valley. This system is powered by

combinatorial Probe-Anchor Synthesis (cPAS), linear isothermal Rolling-Circle

Replication and DNA Nanoballs (DNBTM) technology, followed by high-resolu-

tion digital imaging.

• Guaranteed ≥90% of bases with quality score of ≥Q20

Sequencing

• Typical 35 working days from sample QC acceptance to

filtered raw data availability

• Expedited services are available, contact your local BGI

specialist for details.

Turnaround Time

Project Workflow

SERVICE OVERVIEW

Sample QC

Library QC

LIBRARY

SINGLE CELL

PREPATION

LIBRARY

CIRCUCLARIZATION

SEQUENCING

BIOINFORMATICS

Sequencing QC

We care for your samples from the start through

to the result reporting. Highly experienced labora-

tory professionals follow strict quality procedures

to ensure the integrity of your results.

Request for Information or Quotation

info@bgi.comwww.bgi.com

BGI Americas

One Broadway, 14th Floor

Cambridge, MA 02142,

USA

Tel: +1 617 500-2741

BGI Europe

Ole Maaløes Vej 3,

DK-2200 Copenhagen N,

Denmark

Tel: +45 7026 0806

BGI Asia-Pacific

16 Dai Fu Street,

Tai Po Industrial Estate,

New Territories, Hong Kong

Tel: +852 36103510

Copyright ©2019 BGI. The BGI logo is a trademark of BGI. All rights reserved. All brand and product names are trademarks

or registered trademarks of their respective holders. DNBseq is a trademark of MGI Co. Ltd. Information, descriptions and

specifications in this publication are subject to change without notice.Published Aug 2019.We Sequence, You Discover

• Cell line/tissue/PBMC: After sample processing, freeze cells at a final concentration of 1x106 cells/ml in cryopreserved tubes

(Cell freezing medium: 90% FBS+10% DMSO).

[1] Zhao Y., Li X., Zhao W., Wang J., Yu J.,, Wan Z. & Gao K et al. 2019. Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood.

Gigascience. 5: giz047

BGI 10X Genomics Single Cell Publications

Contact your BGI account representative for the most a�ordable rates in the industry and to discuss how we can meet your

specific project requirements or for expert advice on experiment design, from sample to bioinformatics.

10X GENOMICS S INGLE CELL 3 ’ RNA-SEQ

Data Analysis

Sample Requirements

In addition to raw data output, BGI o�ers a range of standard and customized bioinformatics pipeline for your 10X genomics

single cell sequencing project.

BGI Genomics BGI_Genomics

All Services and Solutions are for research use only.

• Reads extraction: Extract cell-barcodes and UMIs from reads

• Reads alignment: Align short reads to reference genome and transcriptome

• UMI counting: Form a raw-gene-barcode matrix according to UMI number

• Barcoding filtering: Filter those barcodes not from cellular GEM

• Matrix formation: Form filtered gene-barcode matrix

• PCA dimension reduction: Main component analysis (keep most highly variable components)

• Clustering: Graph-based clustering on PCA analysis

• Clustering: Kmeans clustering on PCA analysis

• T-SNE de-dimension: Visualize PAC result in 2D dimension by t-SNE dimension reduction

• DEG analysis: Identify the most significant di�erential expression gene in each cluster

• Generate report: Generate a report in CSV and HTML format

STANDARD ANALYSIS FOR 10X GENOMICS SINGLE CELL 3’ RNA-SEQ