Assay capabilities & Specifications

Our off-the-shelf panels include:

• whole transcriptome

  • human, mouse, and rat

• Surrogate transcriptome

  • human, mouse, rat, and zebrafish

  • bioinformatically designed to include 70-80% of pathways covered by the whole transcriptome with only 4000 probes (maximally diverse expression and minimal co-regulation)

  • particularly useful for large pathway-level screens of biological activity

We can create new, fully custom panels for you, either as subsets of already existing panels, or by designing new probes. This can be include any isoform, mutation (SNP or fusion gene) and species, as long as you are able to provide a reference transcriptome/genome or reliable FASTQ files. We have previously designed custom panels for Drosophila melanogaster, Daphnia magna, and extracellular pathogen DNA, amongst others.

TempO-Seq runs directly from tissue or cell lysates without RNA extraction, purification, or cDNA synthesis. This drastically increases sensitivity, as RNA extraction often causes loss of RNA and may introduce size bias. The assay is based on hybridisation of specific probes to the sample’s RNA in situ, which is a highly efficient and conserved molecular process, providing high TempO-Seq assay sensitivity. Therefore, only minute amounts of sample are needed for a successful assay run.

Example types of input:

• Crude cell lysates

  • e.g. in a 96- or 384-well format

• 2-10 mm^2 of a 4 micron FFpe section

  • can be H&E or antibody stained, as long as reagents are nuclease-free

• sorted fixed cells (ICS-FACS)

• Laser-capture microdissected (LCM) samples from ffpe tissue

• whole blood

• whole zebrafish embryo lysate

TempO-Seq has provided good results from many “difficult” or “low input” samples that are difficult to profile with other established technologies. Sample requirements can be found here, but please feel free to speak to us if you are unsure about your sample type or would like to know more.

As the assay circumvents the steps of RNA extraction/purification (which can result in significant RNA loss), reverse transcription (which is carried out by an enzyme that is evolutionarily designed to introduce errors), and does not require pre-amplification (which can induce bias), TempO-Seq offers excellent accuracy.

Based on highly efficient and sensitive hybridisation of specific probes to regions of interest within a gene, the assay is capable of detecting a lower threshold of ~ 16 molecules and offers high reproducibility down to 10 pg of RNA input (single cell equivalent).

Read TempO-Seq publications here.

Based on the assay biochemistry, TempO-Seq enables high samples multiplexing on the sequencer. This means more samples can be run in the same sequencing run, reducing the sequencing costs per sample drastically.

Therefore, TempO-Seq is enables truly affordable transcriptomic/genomic studies at a large scale. For smaller studies, the same cost benefits will not directly apply, but TempO-Seq is typically cheaper than RNA-seq or other established profiling methods. Importantly, analysis is simplified significantly and data output is a flatfile CSV table outlining gene expression counts per sample. The TempO-SeqR software enables further exploration of the data without requiring informatics knowledge: carry out PCA plots or differential gene expression using an easy-to-use online tool.

Please get in touch if you would like to know more or discuss a project.