RNA Sequencing in 3D spheroids: Engineered for Transcriptomics Discoveries - InSphero

Key ingredients of successful RNA Sequencing study and gene expression analysis in 3D spheroid models

Harness the power of next-generation sequencing (NGS) and unravel secrets of the transcriptome in physiology-relevant in-vitro 3D spheroid models via our all-in-one solution. Seamless project planning and study design are powered by InSphero’s internal know-how served by the experienced InSphero team. High-throughput sample generation is achieved via worry-free, well-established RNA-Seq workflows. Reliable gene expression profiling from biological replicates of single spheroids is accomplished through RNA-Seq technology attuned to low-input material. Project-tailored and gold-standard RNA-Seq data analysis is generated via a dedicated InSphero RNA-Seq analysis pipeline.

A myriad of benefits at your fingertips

  • Precisely address your project-specific questions through a highly flexible and comprehensive RNA Seq service 
  • Obtain more relevant gene expression data by using physiological 3D spheroid models (i.e., 3D InSight™ Microtissues)
  • Minimize technical biases in your RNASeq study by relying on optimized plate layouts and seamless experimental procedures utilizing high-throughput and compatible Akura™ 96-Well Platform
  • Compare numerous intervention groups with stronger statistical relevance via scalable single microtissue RNA-Seq analysis 
  • Increase the complexity of your transcriptomic data analysis step by step using dedicated RNA-Seq Analysis Packages 
  • Extract meaningful gene expression signatures and interpret them with ease thanks to user-friendly data presentation in the interactive RNA-Seq report dashboard

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Get Started – RNA-Seq in 3D InSight™ models

Get an initial consultation about how to leverage 3D InSight™ models and services for high-throughput transcriptomics studies. Just help us understand your topics of interest:
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Whole transcriptome gene expression profiling with TempO-Seq assay

TempO-Seq® (Templated Oligo-Sequencing) by BioSpyder is a novel probe-based approach for very efficient transcriptome-wide profiling. InSphero utilizes Whole Transcriptome  TempO-Seq assay accounting for most of the protein-coding part of a genome. Unlike the standard bulk RNA Seq approach, constructing the RNA sequencing library for TempO-Seq is done from the crude lysate. Since no RNA purification or reverse transcription is needed, the TempO-Seq assay is perfectly suited for low-input material like single 3D spheroids and maximizes the utilization of precious material in the RNA Seq experiment. InSphero generates lysates from single microtissues (i.e., 3D InSight™ Liver Microtissues) or pools of three microtissues (i.e., 3D InSight™ Islet Microtissues) providing unapparelled biological resolution.

Unbiased gene expression assessment with low-input bulk RNA Sequencing technology

To fuel the unconstrained discovery of transcriptomics changes in single 3D spheroid cultures, InSphero is currently establishing devoted workflows for low-input bulk RNA-Seq. We already have some successes in executing it in 3D InSight™ Liver Microtissues. To learn more, please Contact Us.

Get Started – RNA-Seq in 3D InSight™ models

Get an initial consultation about how to leverage 3D InSight™ models and services for high-throughput transcriptomics studies. Just help us understand your topics of interest:
  • This field is for validation purposes and should be left unchanged.

Gold-standard RNA-Seq Analysis Pipeline dedicated to transcriptomics discoveries

High-throughput RNA sequencing experiments yield multi-dimensional data that calls for advanced statistics and sophisticated bioinformatics software to be processed. Therefore, transcriptomics data from gene expression screening performed by InSphero is analyzed via a dedicated RNA-Seq Analysis Pipeline, which facilitates automatic, highly structured and reliable RNASeq data processing. The analysis pipeline is powered by R programming language and a broad range of R libraries regarded the state-of-the-art approaches in transcriptomics data analysis. The analysis pipeline is divided into functional blocks reflecting the analysis stages.

Seamless interpretation of your RNA sequencing results facilitated by an interactive RNA-Seq Analysis Report

InSphero RNA-Seq Analysis Pipeline generates a variety of numeric output and advanced visuals that help to disentangle even the most complex gene expression results. Each of the provided tables or graphics gives instant insight into your multifaceted next generation sequencing (NGS) results. For the most optimal user experience and enhanced accessibility, RNA-Seq analysis results are reported in an interactive report dashboard that embodies features of modern data presentation.

Customer and project-specific analysis of gene expression results enabled by modular RNA-Seq Analysis Packages

To address every budget and project need, InSphero created a transparent offering for services with an RNA sequencing endpoint. For clients who don’t want to generate their own transcriptomics data, we offer Gene Mining Package which gives targeted gene-level insight into existing InSphero internal gene expression data sets. If only a quality assessment of the Client’s raw data with no further transcriptomic analysis is needed, our QC Package is the best choice. Whereas our Basic Package is dedicated to Clients that are interested in unbiased exploration and discovery and seek basic but comprehensive RNA-Seq data analysis, including Differential Expression Analysis (DEA) & Gene Set Enrichment Analysis (GSEA). For our most demanding Clients, we recommend the Extended Package, which expands the transcriptomics findings of the Basic Package by incorporating biological expectations and applying a more guided RNA-Seq analysis approach.

RNA-SEQ ANALYSIS PACKAGES

Gene Mining

QC

Basic

Extended

Study Design Consultancy
Quality Control
Data Exploration
Differential Expression Analysis (DEA)
Gene Set Enrichment Analysis (GSEA)
Gene Mining
Intersecting DEA and GSEA
Visualizing DEA in Pathway Maps
Gene-set Specific Heatmaps
RNA-Seq Report Dashboard

RNA-SEQ ANALYSIS PACKAGES

Gene Mining

QC

Study Design Consultancy
Quality Control
Data Exploration
Differential Expression Analysis (DEA)
Gene Set Enrichment Analysis (GSEA)
Gene Mining
Intersecting DEA and GSEA
Visualizing DEA in Pathway Maps
Gene-set Specific Heatmaps
RNA-Seq Report Dashboard

Basic

Extended

Study Design Consultancy
Quality Control
Data Exploration
Differential Expression Analysis (DEA)
Gene Set Enrichment Analysis (GSEA)
Gene Mining
Intersecting DEA and GSEA
Visualizing DEA in Pathway Maps
Gene-set Specific Heatmaps
RNA-Seq Report Dashboard

Learn more through our recent publications with transcriptomics data obtained from 3D InSight™ Microtissues

Contact Us

Get Started – RNA-Seq in 3D InSight™ models

Get an initial consultation about how to leverage 3D InSight™ models and services for high-throughput transcriptomics studies. Just help us understand your topics of interest:
  • This field is for validation purposes and should be left unchanged.