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

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Tools Digital Droplet System SeekOne DD

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Microfluidic Control SystemSeekMate Tinitan

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Fluoresence Cell Counter SeekOne

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DD Single Cell 3’Transcriptome Kit SeekOne

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DD Single Cell Immune Profiling Kit SeekOne

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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.

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Expedite experimental design

For the researcher in academia and industry

One year trial on one unit of SeekOne® Digital Droplet System, REF: M001A 9000 Euro
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.

SURFSeq 5000* Sequencing Platform
FASTASeq 300* Sequencing Platform
GenoLab M* Sequencing Platform
MrLH-96
Automated Sample Preparation System

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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.

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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

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.
3rd-gen-seq with PacBio/Nanopore is more expensive and has more data limitations than Digital Droplet scFAST seq analyses mRNA
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.

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