Single- nucleus RNA Sequencing

The advance in single cell capturing and individual library construction technique combining with high-throughput sequencing allows gene expression studies on cell-by-cell basis. It enables a deeper and complete system analysis on complex cell populations, in which it largely avoids masking of their heterogeneity by taking average of all cells.

However, some cells are not suitable to be made into single-cell suspension, so other sample preparation methods – nucleus extraction from tissues are needed, that is, nucleus is directly extracted from tissues or cell and prepared into single-nucleus suspension for single-cell sequencing.

BMK provides 10× Genomics ChromiumTM based single-cell RNA sequencing service. This service has been widely used in studies on disease related studies, such as immune cell differentiation, tumor heterogeneity, tissue development, etc.

Spatial transcriptome chip: 10× Genomics

Platform: Illumina NovaSeq 6000

Service Details


Demo Results

Technical principle

The isolation of nucleus is achieved by 10× Genomics ChromiumTM, which consists eight-channel microfluidics system with double crossings. In this system, a gel beads with barcodes and primer, enzymes and a single nucleus are encapsulated in nanoliter-sized oil drop, generating Gel Bead-in-Emulsion (GEM). Once GEM are formed, cell lysis and release of barcodes are performed in each GEM. mRNA are reverse transcribed into cDNA molecules wih 10× barcodes and UMI, which are further subject to standard sequencing library construction.


Tissue not suitable for single cell suspension preparation

Cell / Tissue


Unfresh frozen tissue

Unable to get fresh or long-saved organizations

Muscle cell, Megakaryocyte, Fat…

Cell diameter is too large to enter the instrument


Too fragile to break, unable to distinguish single cells

Neuron cell, Brain…

More sensitive, easy to stress, will change the sequencing results

Pancreas, Thyroid…

Rich in endogenous enzymes, affecting the production of single cell suspension

Single-nucleus vs Single-cell



Unlimited cell diameter

Cell diameter: 10-40 μm

The material can be frozen tissue

The material must be fresh tissue

Low stress of frozen cells

Enzyme treatment may cause cell stress reaction

No red blood cells need to be removed

Red blood cells need to be removed

Nuclear expresses bioinformation

The whole cell expresses bioinformation

Service Specifications


Sequencing strategy

Data recommended

Sample Requirements

10× Genomics single-nucleus library

10x Genomics -Illumina PE150

100,000 reads/cell approx. 100-200 Gb

Cell number: >2× 105

Cell conc. at 700-1,200 cell/μL

For more details on sample preparation guidance and service workflow, please feel free to talk to a 

Service Work Flow

10x (3)

Experiment design

10x (4)

Sample delivery


Nuclear suspension

10x (5)

Library construction

10x (6)


10x (7)

Data analysis

10x (8)

After-sale services

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    1.Spot clustering


    2.Marker expression abundance clustering heatmap

    wps_doc_113.Maker gene distribution in different clusters


    4.Cell trajectory analysis/pseudotime




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