Single-cell RNA

True resolution

For many years, the study of transcriptome dynamics has been carried with tecnologies such as RNA sequencing and microarrays, just to name a few. These techniques usually require several million of cell to yield a pool of template RNA and be subject of the measurement. This, while being an established, robust and cost-effective experimental set-up, provides an averaged sampling of all transcriptomes across a cell population. 

By using stae-of-art technology such those offered by 10X Genomics and Parse Biosciences, IGATech is offering the possibility to move to a new paradigm. The platform is capable of simultaneously tagging hundreds to tens of thousands cell within a single library. After sequencing, reads can be assigned to the original cell and, based on transcriptome profiles, it is possible to distinguish subpopulations, trajectory of development, states as well as to discover associated marker genes. Moreover, oligo-antibody conjugates can be used to selectively tag specific cell types, measure the abundance of certain surface proteins and precisely stratify cells based on their differentiation state. 

Bioinformatics Support

• Primary Analyses: Cell counts, sequencing metrics, gene counts, mapping performances, preliminary clustring and indentification of DE genes across clusters.

• Secondary Analysis
  • Preprocessing and Visualization: custom filtering of cells and genes, feature selection, dimensional reduction, data integration (harmony), normaliazation and scaling.
  • Data integration and correction of batch effect
  • Exploratory Analysis: Clustering and cell group identification - Violin plots per cluster, correlation heatmaps, most variable genes, DE across samples, preliminary (automatic) cell type annotation.
  • Manual cell type annotation
  • Differential expression analysis: differential expression, gene set enrichment and pathway analysis, compositional analysis.

• Advanced Analysis
  • Genere regulatory networks
  • Trajectory analysis (pseudotime and velocity).
  • Integrative single-cell analysis (multiple dataset, pubhlic data, cell atlas, multi-omics analyses).

Cell-plex

When using 10X Genomics products, the basic principle is to tag different samples with specific oligo tags conjugated with non-selective antibodies and then follow standard procedure of sample preparation and sequencing. With Parse bioscience, early segregation in the split-pool barconding process allows to prepare several samples simultaneously. This brings two extremely important benefits:

• All samples are processed in the same experiments removing batch effect.
• A single preparation reagents set is used for several samples, significantly reducing costs.

Fast-track BD Rhapsody library sequencing

In collaboration with BD, IGATech is now offering an expedite sequencing service for RhaposdyTM libraries prepared by end users.

Leveraging availability of two independent platforms (NovaSeq and AVITI), we can provide maximized quality and cost-effectivness in the sequencing of multimodal preparations (whole trascriptome, target panels, AbSeq, SampleTag, TCR and BCR) and any level of cell numer and multiplexing.

If you are interested to enter into the single-cell RNA-seq resolution, we are looking forward to help you.

Contact us and plan your experimental set-up with one of our experts.