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 scRNA seq-guided data

for a successful GEX  single-cell RNA sequencing (scRNA-seq) or gene expression analysis, for gene expression (GEX) studies  and other analyses like proteomics or metabolomics


Instrument Software SeekOne SeekSoul
®
Tools Digital Droplet System SeekOne DD
®
Microfluidic Control SystemSeekMate Tinitan
TM​
Fluoresence Cell Counter SeekOne
®
DD Single Cell 3’Transcriptome Kit SeekOne
®
DD Single Cell Immune Profiling Kit SeekOne
®
DD Single Cell Full-length RNA Sequence Transcriptome-seq (scFAST-seq) Kit  

Approach

The products and services offered are 

SeekOne® Digital Droplet System

M001A

1 unit

unit

SeekSpace® High-Frequency Ultrasonic Device

M005A

1 unit

unit

SeekMate Tinitan® Fluorescence Cell Counter

M002C

1 unit

unit

 

Reagent kit

Product Name

Model

Specification

Unit

SeekOne® DD Single Cell 3' Transcriptome-seq Kit
K00202-08
8 tests
set
SeekOne® DD Single Cell 5' Transcriptome-seq Kit
K00501-08
8 tests
set
SeekOne® DD Single Cell TCR Enrichment Kit (Human)
K00601-08
8 tests
set
SeekOne® DD Single Cell BCR Enrichment Kit (Human)
K00701-08
8 tests
set
SeekOne® DD Single Cell TCR Enrichment Kit (Mouse)
K01101-08
8 tests
set
SeekOne® DD Single Cell BCR Enrichment Kit (Mouse)
K01201-08
8 tests
set
SeekOne® DD Single Cell Full-length RNA Sequence Transcriptome-seq Kit
K00801-08
8 tests
set
SeekOne® DD FFPE Single Cell Transcriptome-seq Kit
K02101-08
8 tests
set
SeekMate FFPE Dissociation Kit
K02301-08
8 tests
set
SeekSpace® Single Cell Spatial Transcriptome-seq Kit
K02501-08
8 tests
set
SeekSpace® Single Cell Spatial Transcriptome-seq Kit
K02501-02
2 tests
set
SeekSpace® Chip Holder
SP00054
1 unit
unit
SeekMate® Tissue Dissociation Kit A Pro
K01801-08
8 tests
set
SeekMate® Tissue Dissociation Kit A Pro
K01801-30
30 tests
set
SeekMate Cell Counter Chip
SP00022
50 pieces
box
SeekMate AO/PI Staining Kit
K01701
5 ml
bottle

. This content is the foundation of our products and services and is managed in SeekBase, the knowledge core of SeekQuence. 

The extensive body of knowledge includes reagents and tools used in the scientific world, what research applications they were used for, by what researchers, purchased from which suppliers, and published in what peer-reviewed publications. Applying computational and analytical methods, SeekQuence established relationships between these different entities.

Products and Services

Product search portal
Expedite experimental design
For the researcher in academia and industry


  1. One year trial on one unit of SeekOne® Digital Droplet System,                         REF: M001A 9000 Euro
  2. SeekOne Single Cell 3’ Transcriptomeseq Kit, 8 tests per kit                            REF:   K00202-08 9000 Euro



SeekProducts is a product search portal, designed with the researcher in mind that needs to quickly identify the right product for the next experiment.
Design the next experiment with a trusted and validated product. Knowing that a product has been successfully used for a specific scientific application by respected scientists, as demonstrated by a peer-reviewed publication, is of great importance to any researcher.


Search across a vast amount of product suppliers - supplier-agnostic
Find products based on research area of interest

UMI counts represent the absolute number of observed transcripts (per gene, cell or sample). As absolute counts, they are not normalized for sequencing depth, technical variation or RNA content per cell.


Filter down to relevant products via a comprehensive set of facets
Quickly identify any publication and researcher that has successfully used the scRNA Digital Droplet seq strategy of interest with longest reads like Seekgene

Find relevant GSEA that employs differentially expressed genes between sample groups for functional enrichment analysis, whereas GSVA estimates the variations in gene set enrichment for each sample based on the expression profiles to elucidate functional enrichment differences between sample groups  

Cloud Analysis with SeekSoul a web-based application that is stronger than Cell Ranger and Space Ranger from 10x Genomics' cloud.


SeekOne DD scFAST-seq is better than the Nanopore 3th generation


  1. Digital Droplet scFAST seq can analyse mRNA, lncRNA, viral RNA, mRNA, lncRNA (with polyA) Analysis dimension Gene expression Gene expression SNP/InDel mutation Gene fusion Non coding RNA regulation Pathogen transcripts such as viral RNA Alternative splicing.
  2. 3rd-gen-seq with PacBio/Nanopore is more expensive and has more data limitations than Digital Droplet scFAST seq analyses mRNA
  3. BOTH CAN ANALYSE Long non-coding RNA (lncRNA) are RNA transcripts over 200 nucleotides in length that do not encode proteins. This is a broad definition, encompassing around 270 000 unique RNA in humans, although only 15000 have so far been functionally annotated






SeekOne Digital Droplet (SeekOne DD) Higg throughput Single Cell Full-length RNA Sequence Transcriptome-seq (scFAST-seq) Kit


High-throughput whole transcriptome profiling. The scFAST-seq method makes use of innovative techniques

including semi-random primers, efficient reverse transcription, template swapping, and effective rRNA removal to build full-length RNA libraries of up to 12,000 cells. 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. The kit is designed to be used in conjunction with our SeekOne Digital Droplet System (SeekOne DD)


We compared SeekOne DD scFAST seq with the 3' 10x single cell data from a 3' expression kit. The poly(dT)VN captures the end of the transcript and one can sequence 150 bp. While visualizing BAM file in IGV. I filtered the BAM file to only include reads used for UMI counting.


 You will only  be sequencing 150 bp and only expect to see reads aligning to maybe the last two exons of a transcript?


That is why Seekgene offers to complete the entire process from single-cell nucleic acid labelling to transcriptome library construction. When equipped with "SeekSoul Tools", our single-cell data analysis software, we provide a one-stop-shop single-cell transcriptome solution.







Functions of the RSeQC tool are called (incl. the gene coverage plot)

Having said this, in the past I came across an R package called genecovr (link) that based on the available info might do what you are looking for ("The genecovr package provides functionality for evaluating gene body coverage and other metrics in genome assemblies. The central measurement unit is a gene or transcript model"). Also see the vignette.

gene body coverage

Also, I know that the R package accompanying the QoRTs tool is used to make visualizations of QC metrics, including gene coverage plots. Again, I don't have any hands-on experience with it, so I cannot comment on its compatibility with your output files...

<<forgot to add>> When browsing Bioconductor packages I also noticed the package CoverageView. Although primarily designed for the visualization of ChIp-seq-like experiments, "additionally, CoverageView can also be used in RNA-seq experiments in order to compare how the coverage is distributed along the transcriptome."

  Azenta

Bio Molecular Systems

Biolidics

Bioptic Inc

Bioscreen

Byonoy

Catch Gene

CEM

Denovix

Gesim

Iota Sciences

Levitas Bio

Nano Analytics

Nicoya

PAA – Peak Analysis & Automation

Porvair Sciences

Proteome Software

RBC Bioscience

S2 Genomics

SeekGene

Yokogawa

Zybio

Find antibodies for different model organism - beyond human antibodies
Initial focus is antibody products, but other product categories (e.g. NGS products) are coming soon.