SINGLE CELL ANALYSIS UNIT

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Technical information for sample collection

Single Cell Multiomic Analysis

Single Cell Sorting & Barcoding

Chromium Controller 10X

Experimental Design

We help you design the right experiment for your sample type. We are equipped to advise you on the best way to get started with both experimental set up and sample preparation in order to meet the necessary QCs for the 10X Genomics.

Sample processing

The sample is prepped in our lab and loaded subsequently onto the 10X Genomics Chromium microfluidics controller for high throughput barcoding. Here, the individual cells are combined with barcoded gel beads and oil drops. After the barcoding of individual cells the samples are library prepped for next generation sequencing.

Services description

With the Chromium Controller and the microfluidic chips, thousands of cells per sample are barcoded and prepped for analysis. Use the PmedGR 10x Genomics services for gene expression profiling– RNA sequencing or chromatin profiling-ATAC sequencing at single-cell level

Chromium Single Cell Gene expression Analysis

The SC-RNAseq contributes to the gene expression profiling of hundreds of thousands of cells and allows to detect unique transcripts per cell. SC-RNAseq provides us with the capacity to characterize cell populations, cell types, cell states and more on a cell-by cell basis. The Chromium Single Cell Gene Expression kit, allows us to create highly complex libraries from single cells in order to maximize insight from any sample type. The SC-RNA-se can be used to:

Identify and characterize rare cell types
Analyze and understand cell heterogeneity
Perform cellular phenotyping in order to identify novel cell surface markers and biomarkers
Assess comprehensive gene expression phenotyping for individual CRISPR perturbations

Chromium Single cell ATAC (Assay for Transposase Accessible Chromatin) sequencing

Reveal Chromatin accessibility with Single cell epigenomics

SC-ATAC seq, contributes to our understanding of the regulatory landscape of the genome, thus providing insights into cell variability and regulation of gene expression at high resolution. The SC-ATACseq can be used to :

Study developmental plasticity
Discover cellular heterogeneity stemming from epigenetic variability
Uncover gene regulatory networks that are upstream of gene expression
Define cell types and states for lineage and developmental tracing
Accelerate biomarker discovery

How does it function?

Single cell 3’ RNAseq workflow

10x single-cell 3' partition individual cells into GEMs that uniquely barcode hundreds to thousands of cells with a capture efficiency of 65%. 3’ end counting determines gene expression and characterizes cells of a heterogeneous population. 3' assay can be combined with "Feature Barcoding" technology which determines expression of cell-surface proteins through oligo-labelled antibodies. For more information about these assays, please visit 10xGenomics.

Single cell ATAC workflow

The single cell ATAC assay allows for determination of the accessibility of chromatin on a single cell level. A sample of hundreds to thousands of nuclei undergoes a transposition reaction and the transposed nuclei are then partitioned into GEMs which uniquely barcode accessible DNA fragments. For more information about this assay, please visit 10xGenomics.

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