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SeekOne Chromium comparative study

10x Genomics was compared to the SeekGene scRNA seq Seekone Instrument 


Seekgene V(D)J recombination (variable–diversity–joining rearrangement) for somatic recombination that occurs only in developing lymphocytes during the early stages of T and B cell maturation. It results in the highly diverse repertoire of antibodies/immunoglobulins and T cell receptors (TCRs) found in B cells and T cells, respectively. The process is a defining feature of the adaptive immune system.
V(D)J recombination in mammals occurs in the primary lymphoid organs (bone marrow for B cells and thymus for T cells) and in a nearly random fashion rearranges variable (V), joining (J), and in some cases, diversity (D) gene segments. The process ultimately results in novel amino acid sequences in the antigen-binding regions of immunoglobulins and TCRs that allow for the recognition of antigens from nearly all pathogens including bacteria, viruses, parasites, and worms as well as "altered self cells" as seen in cancer. The recognition can also be allergic in nature (e.g. to pollen or other allergens) or may match host tissues and lead to autoimmunity.
Chromium Xo is a high-performance single cell scRNA seq

It uses GEM-X technology for 3’ whole transcriptome profiling, Chromium Xo.



Why Seekgene's Single Cell 3' Transcriptome kit called scFAST seq is better?

—— Investigate gene expression with accuracy and efficiency

SeekOneDD (Digital Droplet) Single Cell 3' Transcriptome-seq is a high-throughput single-cell RNA-seq library kit achieves single-cell partitioning and labelling by the microfluidic system and barcoded beads. The kit needs to be used with the SeekOneDigital Droplet System (SeekOneDD) to complete the whole process from single-cell transcriptome barcoding to library construction.

 

SeekOneDD single cell 3' transcriptome kit includes: SeekOneDD Chip S3 (Chip S3 for short), Gasket, Carrier Oil, SeekOneDD 3' Barcoded Beads (Barcoded Beads for short), amplification reagents, library construction reagents, and single cell data analysis software (SeekSoulTools). 



Based on the principle of microfluidic technology, the kit uses emulsion droplets to separate and capture individual cells, and then recruits nucleic acid-modified Barcoded Beads to molecularly label RNA from different cell sources. Finally, a high-throughput single-cell transcriptome library compatible with Illumina and MGI sequencing system will be constructed, which can be used for research on tumors, immunity, cell development, viral infections, drug discovery, and target screening, etc.

1. Seekgene has better Single cell capture and labelling

 

Cells and barcoded beads are added separately and then react in the carrier oil to form emulsion droplets in the -shaped channel. After that, mRNA molecules released by the cells are captured by oligo(dT) on the barcoded beads.

  • Workflow 
  • Product Features

Compare Compatible Instrument


SeekOneDD is much liter and better pricing than Chromium X

Lieven Gevaert, Bio-ir at Gentaur Institute Leuven Belgium

1-8samples can be flexibly run at a time

500-12,000 cells can be captured with a single channe 150,000

emulsion droplets can be generated in 3 minutes


Recovery of ~1000 cells with

doublet rates of

~0.3% per 1,000 cells

2. Seekgene has an Unlimited Library Construction

● Compatible

 

Compatible with single cell 3' transcriptome sequencing (3' scRNA-seq) and single nucleus RNA sequencing (snRNA-seq). Dual index libraries compatible with both Illumina and MGI sequencers.

 

 

● Seekgene is Faster than 10x

 

Rapid generation of 150,000 water-in-oil droplets in 3 minutes with high success

rates, especially for precious and sensitive samples.

 

 

● Seekgene is more Cost-saving compared to 10x Chromium

 

Unique place chip design eliminates chip waste, reducing operation time and cost

 

 

● Suitable sample types

 

a. Delicate samples with low cell viability:brain tissue, retinal tissue, all tissues from aged individuals 

b. Tissues requiring nuclei isolation: frozen tissues, pancreatic tissues, neurons, adipose tissue, etc. 

c. Larger cohort or atlas studies where multiple samples need to be processed simultaneously.




SeekOneDigital Droplet System

Reverse transcription

Template conversion and extension

Fragmentation and end repair

connector connection

library amplification


SeekOneDD

Single Cell 3' Transcriptome kit

SeekOneDigital Droplet System

SeekSoul Tools

Seekgene has better Reagents

More capable Instrument


Seekgen has better Software

SeekOneDD

Single Cell Immune Profiling Kit

SeekOneDD

Single Cell Full-length RNA Sequence Transcriptome-seq kit

cDNA amplification

High cell capture rates of up to 65%

Order Information

Product Name

Cat.No.

Specification

SeekOne® DD Single Cell 3’  Transcriptome-seq Kit


in Gentaur  we work to make single cell more accessible at lower costs, Chromium Xo is just the start. New Chromium innovations are coming soon, continuing our commitment to provide superior performance over alternative methods and reduce budget constraints at every step. What does that look like in your lab? Find out below.

The next generation of single cell is here

Introducing Chromium Single Cell Gene Expression v4 and Single Cell Immune Profiling v3, powered by new GEM-X technology

  • Partition and barcode your cells 3x faster
  • Achieve cell recovery efficiency rates of up to 80%
  • Reduce multiplet rates two-fold
  • Lower sequencing costs by up to 50%

L

Uncover new insights

Discover cellular diversity, rare cells, and disease-linked cell types.

Single cell immune profiling fuels biomarker discovery in cancer samples

Check out three separate studies from researchers at Columbia University and MD Anderson that provide impactful insights into cancer research.

Rpostead blog post

Single cell multiomics reveals kidney cell behind erythropoietin, master regulator of red blood cell production

Explore a recent Nature Medicine publication, where researchers used single cell transcriptomic and epigenetic analyses to identify the cell type behind the production of erythropoietin, opening up anemia treatment possibilities.

Read

Organoids bring drug discovery and development to the culture hood

Explore the work of four research teams using single cell RNA-seq and organoids to identify druggable pathways in liver disease, screen drugs for kidney disease, model drug metabolism in the liver, and study therapeutic responses in oncology patient-derived models.

R

Capture RNA, protein, chromatin and more

Get a complete picture with versatile assays that profile multiple analytes.


Compare single cell assaysAll (5)Gene Expression (4)B-cell or T-cell receptors (1)Chromatin accessibility (2)Cell surface protein (3)

Probe-based gene expression for fresh, frozen, and FFPE samples

What is a FFPE sample?

Formalin-Fixed Paraffin-Embedded sample

Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens have been a staple of research and therapeutic applications for decades. FFPE is a form of preservation and preparation for biopsy specimens that aids in examination, experimental research, and diagnostic/drug development.

Our most sensitive whole transcriptome analysis with the flexibility to fix, batch, and run samples on your schedule.

Single Cell Gene Expression Flex

3' gene expression

A versatile solution providing 3' transcriptomic profiling with options for multiomic analysis.

Single Cell Gene Expression

5' gene expression with immune repertoire profiling

Assay with multiomic capabilities and options for comprehensive analysis of immune diversity, including BCR or TCR repertoire profiling.

Single Cell Immune Profiling

Chromatin accessibility and gene expression from the same nucleus

Simultaneously profile the transcriptome and epigenome at single cell resolution.

Single Cell Multiome

Chromatin accessibility

Analyze thousands of unique open chromatin fragments per cell with scATAC-seq.

Single Cell ATACAdditional capabilitiesAll (3)Compatible with Gene Expression (3') (2)Compatible with Immune Profiling (5') (3)

Directly link CRISPR guide RNAs to the resulting perturbed phenotypes

CRISPR Screening

Capture protein alongside gene expression to better characterize complex biology

Multiomic Cytometry

Accelerate therapeutic discovery with rapid, antigen-specific clonotype identification

Barcode Enabled Antigen Mapping

Get the instrument-supported Chromium advantage


  • Automate the most critical steps for more reproducible results and a lower risk of manual error than with instrument-less methods
  • Ensure high success rates and consistent performance, with a demonstrated R2 value of 0.97 across runs, users, and timepoints
  • Partition tens of thousands of cells in mere minutes, saving on time and labor costs with 1-day workflows and just 3–4 hours of hands-on time
  • Use our intuitive push-button interface for efficient cell processing without the hassle of cumbersome pipetting methods

PRODUCTS

 

Single Cell Full-length RNA Sequence Transcriptome-seq kit

—— The Time Has Come for A New Generation of Single Cell Transcriptome Profiling

SeekOneDigital Droplet (SeekOneDD) High throughput Single Cell Full-length RNA Sequence Transcriptome-seq (scFAST-seq) Kit, self- developed by Beijing SeekGene BioSciences Co., Ltd., is a powerful commercial tool for high-throughput whole transcriptome profiling. Compared to conventional 3' scRNA-seq, scFAST- seq has distinct advantages in detecting non- polyadenylated transcripts, transcript coverage length, and identification of more splice junctions. With target region enrichment, scFAST-seq can simultaneously detect somatic mutations and cell states in individual tumour cells, providing valuable information for precision medicine.

SeekOneDD Single Cell Full-length RNA Sequence Transcriptome-seq (scFAST-seq) Kit includes SeekOneDD Chip S3 (Chip S3), Gasket, Carrier Oil, SeekOneDD scFAST-seq Barcoded Beads, amplification reagents, library construction reagents.

Using microfluidic digital droplets and Barcoded Beads coupled with random primers, single-cell partition and random capture of the whole transcriptome can be achieved in a step of generating water-in-oil droplets. This convenient process requires only a small amount of sample. The inclusion of an rRNA blocker enables efficient depletion of rRNA, delivering higher proportion of effective data.

Core technology and workflow

Compatible Instrument


SeekOneDD

SeekOneDigital Droplet System

SeekOneDD

Single Cell 3'Transcriptome-seq kit

SeekOneDigital Droplet System

SeekSoul Tools

 

Reagent 

Instrument

Software

 

SeekOneDD

Single Cell Immune Profiling Kit

 

SeekOneDD

Single Cell Full-length RNA Sequence Transcriptome-seq kit

Detection of single cell mutation

Order Information

1-8 samples can be

flexibly run at a time

500-12,000 cells can be captured with a single channel 

150,000 emulsion droplets can be generated in 3 minutes

Recovery of ~1000 cells with doublet rates of ~0.3% per 1,000 cells

Even coverage of the full-length of the gene from 5' to 3'end

Seekgene Product Features

Seekgene  More Accurate single-cell transcriptome: Achieve full-length transcriptome detection without being limited by the 3' or 5' end.

Genotype to phenotype:: Simultaneously obtain single-cell mutation and gene expression information, establishing the relationship between genotype and phenotype.

Better Capturing non-coding RNA: In addition to mRNA, non-coding RNA without 3' polyA tails can also be captured.

Crossing the species barrier: Enable the detection of viruses and prokaryotes.

Improving analysis accuracy: Allow the detection of isoform switching events of mRNA and IncRNA.

Applications

Detection of more splice junctions

Identification of non-polyA tailed viral infected cell clusters

Flexibility to incorporate a panel for detecting target genes with high

Achieving effective rRNA depletion: the inclusion of an rRNA blocker enables efficient depletion of rRNA, delivering higher proportion of effective data.

Compared to conventional 3' scRNA-seq, scFAST- seq has distinct advantages in detecting non- polyadenylated transcripts, transcript coverage length, and identification of more splice junctions. With target region enrichment, scFAST-seq can simultaneously detect somatic mutations and cell states in individual tumour cells, providing valuable information for precision medicine.

Clearer and more accurate cell trajectory inference compared to the 3' platform

scFAST-seq data can be integrated with 3' data

Product

Cat.No.

Specification

SeekOne® DD Single Cell Full-length RNA Sequence Transcriptome-seq (scFAST-seq)K00801-088 tests


PRODUCTS

 

Single Cell Immune Profiling Kit

—— Reveal the immune specificity with complete V(D)J sequences

SeekOneDD single-cell immune profiling (5' transcriptome & immune repertoire sequencing), proposed by Beijing SeekGene BioSciences Co., Ltd., achieves single-cell partitioning and labelling by the microfluidic system and barcoded beads. The library of both full-length TCR/BCR sequences and mRNA sequences can be constructed from a single sample, followed by high-throughput sequencing and bioinformatics analysis. 

The SeekOne DDSingle Cell Immune Profiling Kits include the SeekOneDD Single Cell 5’ Transcriptome-seq Kit and the SeekOneDD TCR/BCR amplification Kit. With this kits, the full-length sequence of V(D)J, the pairing information of α chain (heavy chain) and β chain (light chain) of TCR(BCR) and the transcriptome information can be obtained simultaneously. It can be used to investigate T/B cell heterogeneity, TCR/BCR diversity, antigen specificity, vaccine development, immunetherapy screening, etc.

1.Single cell capture and labelling

 


 

SeekOneDD single cell immune profiling products are based on the principle of microfluidic technology. Cells and barcoded beads are added separately and then react in the carrier oil to form emulsion droplets in the - shaped channel. After capturing mRNA tagged with barcoded beads, two separate libraries (gene expression & immune repertoire) can be constructed from a single sample.

Core technology and workflow

Compatible Instrument

Learn more >

SeekOneDD

SeekOneDigital Droplet System

SeekOneDD

Single Cell 3'Transcriptome-seq kit

SeekOneDigital Droplet System

SeekSoul Tools

Reagent 

Instrument

Software

 

SeekOneDD

Single Cell Immune Profiling Kit

 

SeekOneDD

Single Cell Full-length RNA Sequence Transcriptome-seq kit

Up to 90%of reads mapped to any V(D)J gene

Rapid generation of 150000 water-in-oil droplets in 3 minutes 

Flexible running of 1~8 samples in parallel

High cell capture rates of up to 65%

Efficiently capture 500-12,000 cells per channel

Low doublet rates of under 0.3% per 1,000 cells

2.Library construction

Product Features

Full length

 

Complete coverage of the full-length V(D)J sequences. Analyze all V(D)J sequences, including CDR3 sequences, for more comprehensive information

True alignment 

 

True representation of α/β (light/heavy) chain pairing information of TCR (BCR). Reports pairing information from the same cell to reveal receptor-antigen specificity of the immune cells

Efficient capture 

 

Efficiently capture V(D)J sequences with an alignment rate greater than 90%. Obtain more accurate and authentic capture data

One sample with two profiles

 

Simultaneous profiling of immune repertoire (BCR/TCR) and 5’ gene expression Multiple libraries are constructed from a single sample, which is more economical and suitable for samples with limited amounts, such as needle biopsy samples.

Order Information

Product Name

Cat.No.

Specification

SeekOne® DD Single Cell 5’ Transcriptome-seq Kit

K00501-08

8 tests

SeekOne® DD Single Cell TCR Enrichment Kit (Human)

K00601-08

8 tests

SeekOne® DD Single Cell BCR Enrichment Kit (Human)

K00701-08

8 tests

SeekOne® DD Single Cell TCR Enrichment Kit (Mouse)

K01101-08

8 tests

SeekOne® DD Single Cell BCR Enrichment Kit (Mouse)

K01201-08

8 tests


SeekOneDigital

Droplet System

Fast

Rapidly generates 150,000 water-in-oil droplets in 3 minutes, reducing cell loss.

Efficient

Up to 12,000 cells can be captured in a single channel. Flexible running of 1~8 samples in parallel. 

Accurate

Low doublet rates of less than 0.3% per 1,000 cells; equipped with a temperature control system to eliminate the effects of environmental temperature differences.

Compatible

Highly compatible system with a real-time remote upgrade can be used with comprehensive SeekOneproduct lines to meet a variety of scientific research needs. 

SeekOneDD Chip Holder

Chip Holder, used with SeekOne® digital droplet 

system and supporting chips

Product Features

Placed Chip

 

Placed Chip (Chip P for short), placed in a Chip Holder (8 Chip Ps are attached to each instrument);

When the sample throughput   is less than 8, Chip P is placed in the wells 

User-friendly

Small instrument with large screen; 7" + 45° view touch interface makes “one-click” operation more convenient and comfortable.

SeekOne Digital Droplet System

SeekSoul Tools

Reagent 

Instrument

Software

SeekOneDD

Single Cell 3 'Transcriptome-seq kit

SeekOneDD

Single Cell Immune Profiling Kit

SeekOneDD

Single Cell Full-length RNA Sequence Transcriptome-seq kit

Cells and barcoded beads are added separately and then react in the carrier oil to form emulsion droplets in the -shaped channel. After that, mRNA molecules released by the cells are captured by oligo(dT) on the barcoded beads.

Workflow

The process begins with the collection of single cell suspension. After single cell partitioning, capture and labelling, a single cell library compatible with Illumina and MGI sequencers is constructed for high-throughput sequencing. Data can be processed using SeekSoul® Tools ——the efficient data analysis software to explore cell heterogeneity. 

Product Specifications

Flexible cell diameter of 5~40 μm

Rapid generation of 150000 water-in-oil droplets in 3 minutes 

Efficiently capture 500-12,000 cells per channel

Flexible running of 1~8 samples in parallel

High cell capture rates of up to 65%

Low doublet rates of under 0.3% per 1,000 cells

Cost-saving

Vacant channels can be occupied by Place Chip without wasting chips.

Instrument

Cat.No.
SeekOne® Digital Droplet SystemM001A

SeekOne Chip Holder 

SeekOne Chip Holder is the chip holder of the SeekOne MM Single Cell Transcriptome Kit and

is used in conjunction with the SeekOne Chip.

Chip fixture

Product Performance

1 to 4 chips can be placed at a time, and a single operator can process 1 to 4 samples simultaneously.


SeekMate Tinitan

SeekMate Tinitan Fluorescence Cell Analyzer (SeekMate Tinitan FL) is an efficient fluorescence cell analyzer independently developed by SeekMate Biotechnology based on bright field and fluorescence field dual modes. This product uses the latest optical components with dual focusing modes to obtain clear pictures, and introduces AI deep learning. Personalized parameter adjustment provides accurate and stable cell counting solutions for more cell types (including primary cells and cell nuclei). At the same time, the machine is lightweight and compatible with mobile power supplies, which is convenient to carry out and can be used to perform cell counting in any cell laboratory. The device is compact and fully functional. It is a trustworthy handheld "counting expert" with accurate counting, information dimension expansion, and flexibility and convenience.

Fluorescence cell analyzer


Product Advantages

Reagent test kit

equipment

software


  1. SeekMate  Dissociation Kit
  2. SeekOne DD
  3. Single Cell 3' Transcriptome Kit
  4. SeekOne DD
  5. Single Cell Whole-Sequence Transcriptome Kit
  6. SeekOne DD
  7. Single Cell Immunoassay Kit
  8. SeekOne DD
  9. FFPE Sample Single Cell Transcriptome Kit
  10. SeekOne Chip Holder
  11. SeekOne Digital Droplet Meter
  12. SeekSoul CMDB Database
  13. SeekSoul  Tools  Analysis Software
  14. SeekOne MM

  1. Large-pore high-throughput single-cell transcriptome kit

SeekMate Tinitan        Fluorescence Cell Analyzer

TM

SeekSoul  Tools

Products & Technologies

Analysis software

SeekSoul  Tools is a set of software independently developed by SeekSoul Biotechnology to process single-cell transcriptome data. It is used to identify cell label barcodes, compare and quantify, obtain cell expression matrices that can be used for downstream analysis, and then perform cell clustering and differential analysis. The product not only supports the output data of the SeekOne series of kits, but also supports various custom design structures through the description of barcodes.

Analysis Process

Is SeekSoul  Tools compatible with third-party software such as Seurat?

Frequently asked questions

SeekSoul Tools is a single-cell data analysis software independently developed by SeekSoul. It is used in conjunction with the SeekOne®MM/DD single-cell transcriptome library kit. It can only be used after installation under the Linux system. The customer needs to have computing resources and a certain bioinformatics foundation. This software package can complete the basic quality control of offline data. The software has good performance and is compatible with data from a variety of single-cell technology platforms. In addition,  the cell-gene expression matrix obtained by SeekSoul Tools analysis can also be directly imported into third-party software such as the Seurat software package for subsequent analysis.

View more>

SeekSoul CMDB

SeekSoul CMDB is a single-cell omics marker gene database established by SeekSoul Biotechnology. It contains the marker genes used to annotate cell types in currently published single-cell sequencing articles on diseases and healthy tissues. Combined with the automatic annotation software developed by SeekSoul Biotechnology, it can assist in cell type identification and annotation.

database