The power of Clariom assays

Recent advanced transcriptome analyses have uncovered thousands of splice variants and long non-coding (lnc)RNAs, providing new sources for biomarker discovery. Given the complexity of the transcriptome, however, finding informative expression biomarkers is challenging, time-consuming, and costly. Clariom assays, built using the latest transcriptome knowledge from multiple databases, are simple and fast tools for finding high-fidelity expression biomarkers. They are compatible with clinical research samples, available in scalable formats for different throughput needs, and include flexible, intuitive software for fast and simple analysis.

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Designed to provide the comprehensive coverage you need, the reproducibility you require, and the insights you want to act quickly on your discoveries.

Comprising arrays, reagents, and intuitive analysis software, Applied Biosystems Clariom assays deliver comprehensive transcriptome-wide results quickly and easily—even with challenging samples:

From sample to answer, quickly

  • Free, simple, and quick data analysis—Transcriptome Analysis Console (TAC) Software easily analyzes transcriptomic data from all of our Clariom assays, at no additional cost
  • Confidently identify complex biomarker signatures and investigate significantly altered pathways
  • Gain important insights quickly from large-scale cohort studies

Get the data you need, easily

  • Deep and broad transcriptome analysis—Clariom D assays enable rapid discovery of coding and long non-coding genes, exons, splice variants, and rare transcripts 
  • Simple and swift discovery—Clariom S assays provide easy identification of gene-level signatures and pathways from well-annotated genes
  • Reliable, scalable arrays delivering meaningful results in just three days

When you have precious or challenging samples

  • Generate expression profiles from as little as 100 pg of total RNA—as few as 10 cells
  • Analyze RNA from a wide variety of sample types including cells, whole blood, and fresh/fresh-frozen or FFPE tissues
  • Preserve sample integrity and reduce variability with no need for globin or ribosomal RNA removal”

The evidence

With increased knowledge of the transcriptome, a growing body of evidence has implicated lncRNAs as critical regulators of coding RNA and alternative splicing. Aberrant expression of these regulatory lncRNAs has been increasingly documented in a wide range of diseases, establishing their potential for future use as biomarkers and therapeutic agents. 

Transcriptome-level assays identified dysregulated lncRNAs in human gastric epithelial cells infected with Helicobacter pylori

Figure 1. 13 candidate dysregulated lncRNAs identified by transcriptome-level assays were validated by qRT-PCR. Of those, eight samples expressed statistically significant differences in infected (T) vs. control (C) cells. qRT-PCR validation of the same eight samples revealed four lncRNAs that were significantly differentially expressed in H. pylori-positive (P) vs. H. pylori-negative (N) cells. Zhu, H., et al. Microarray analysis of long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori infection. BMC Medical Genomics 8:84 (2015).*

Microarray analysis reveals vital laternative splicing variants in endocrine-resistant breast cancel model cell lines

Figure 2. HTA & Clariom D human arrays deliver the equivalent accuracy in gene expression measurements throughout the transcriptome as sequencing a sample across 2 full lanes on a HiSeq™ 2000 System.  By evaluating a linear tissue mixture model in which RNA from 2 samples are mixed in known proportions, the accuracy of expression was evaluated across all measured exons. The y-axis is the calculated error or, mean absolute deviation (MAD), (median(|x - median(x)|) of (D-C)/(B-A)) where A = Universal Human Reference RNA (UHRR), Agilent Technologies, Inc.; B = Human Brain Reference RNA (HBRR), Life Technologies, Inc.; C = 75%A/25%B; and D = 25%A/75%B.. Array MAD was calculated from all combinations of n = 3 arrays per sample, where n = 4 arrays per sample were available. Box plots display all 256 possible combinations of n = 3 arrays per sample, with box plot whiskers representing the min and max MAD value. Array target was prepared using the GeneChip WT PLUS reagent kit from 100ng of total RNA.

An assay for every need

Whether you need a deep and broad high-resolution transcriptome profile, or are focused on gene-level changes on the surface of the transcriptome, Clariom assays generate reproducible data and offer the level of coverage you need to find biomarkers. Fast analysis yields results. Now.

  Clariom D Assay Clariom D Pico Assay Clariom S Assay Clariom S Pico Assay
Application(s) Deep and broad transcriptome analysis and biomarker discovery Gene-level expression profiling of well-annotated genes
Level of analysis Coding and noncoding genes, exons, and alternative splicing, including both well-annotated and speculative transcripts Well-annotated genes
FFPE tissue– compatible No Yes No Yes
RNA input minimum 50 ng 0.1 ng (0.5 ng for FFPE) 50 ng 0.1 ng (0.5 ng for FFPE)
Part of gene measured

Whole transcript

Available format(s) Cartridge (single sample) Cartridge (single sample) Array plates (24 or 96 samples)
Available species

Human, mouse, rat

Assay kit includes • Clariom D Array
• GeneChip WT PLUS Reagent Kit
• Clariom D Array
• GeneChip WT Pico Kit
• Clariom S Array
• GeneChip WT PLUS Reagent Kit
• Clariom S Array
• GeneChip Pico Kit
Instrument (array format) GeneChip Scanner 3000 7G System (cartridge) GeneChip Scanner 3000 7G System (cartridge) GeneTitan Multi-Channel (MC) Instrument (plates)

Figure 3. TAC Software WikiPathways integration view. Identify a greater number of relevant and differentially expressed genes with pathway visualizations.

Go deep into the transcriptome with Clariom D assays

  • Perform comprehensive and detailed analysis of coding and non-coding genes, exons, and splice variants.
  • Get coverage of all known transcripts, regardless of abundance.
  • Rapidly discover complex signatures and help ensure biomarkers are not missed.

Keep biomarker discovery simple and swift with Clariom S assays

  • Rapidly generate robust expression profiles from all well-annotated genes.
  • Identify important gene signatures and pathways quickly and easily.
  • Discover gene-level signatures and quickly screen large numbers of samples with high-throughput, automated formats.

Extract information from challenging samples with Pico assays

  • Generate expression profiles from as little as 100 pg of total RNA with as few as 10 cells
  • Analyze RNA from a wide variety of sample types, including cells, whole blood, and fresh/fresh-frozen or formalin-fixed, paraffin-embedded (FFPE) tissues
  • Preserve sample integrity and reduce variability with no need for globin or ribosomal RNA removal

Clariom assays are available for human, mouse and rat, with Pico reagents for challenging samples, and in various throughput formats to meet your applications needs. Custom designs are available for other species.

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