Sample Processing Workflow

Asuragen’s sample processing workflows are designed to maximize data quality and minimize turn-around time. As a client-oriented service provider, our clients benefit from a transparent and accessible process that allows them the flexibility to submit a variety of different sample types and receive customized data output.

All our workflows feature process controls, certainty of extensive operator qualification, and our Data Quality Guarantee.

Sample prep workflow

All samples are received and entered into the isolation queue under a controlled SOP to confirm package/sample integrity, appropriate shipping conditions (frozen samples/dry ice, as appropriate), and individual confirmation of sample identity against the shipping manifest and electronic sample submission documents

Standard RNA isolation quality control criteria include yield, purity, and integrity. All Asuragen isolation protocols are qualified by these criteria in addition to RNA stability, endonuclease and exonuclease contamination, and residual DNA contamination measurements. These additional QC measures are also available for your RNA isolations at an additional charge. Unless noted, all RNA isolation methods are optimized to recover miRNA.

Typical yield, purity, integrity and stability data on a wide variety of tissues and cell lines are available for inspection. (more info)

Affymetrix or Illumina gene expression profiling workflows:

  • Incoming total RNA QC (click here for sample prep services):
    • Quantitation and estimation of RNA purity using NanoDrop spectrophotometer readings at 260 and 280 nm
    • Assessment of RNA integrity using Agilent 2100 Bioanalyzer to measure RNA integrity number (RIN) for RNA prepared by Asuragen (not applicable for FFPE samples)
    • See our Sample Submission Form and Shipping Instructions for recommended incoming sample QC values
  • Target preparation, specific to the array/probe platform followed by cRNA QC
  • Array hybridization, washing, and scanning followed by array QC
  • Data summarization (additional analysis services)

Agilent or Ambion/Affymetrix DiscovArray miRNA expression profiling workflows:

Applied Biosystems miRNA and mRNA TaqMan® workflows:

  • Incoming RNA QC by NanoDrop and Agilent Bioanalyzer
    • Quantitation and estimation of RNA purity using NanoDrop spectrophotometer readings at 260 and 280 nm
    • qRT-PCR assessment of discrete miRNAs or housekeeping genes as a surrogate measure of overall miRNA or mRNA abundance
    • See our Sample Submission Form and Shipping Instructions for recommended incoming sample QC values
  • Reverse-transcription by miRNA-specific priming, or by random priming (default), oligo-dT priming, or gene specific priming
  • Real-time detection via TaqMan primer & probe technology in triplicate for single miRNA assays, or as defined by array format

Agilent aCGH workflow:

  • Incoming DNA QC (click here for sample prep services):
  • Target preparation and enzymatic labeling
  • Combined labeled experimental and reference genomes
  • Data extraction and analysis using Agilent’s Feature Extraction Software

Non-FFPE samples enter the workflow at target prep stage.

Bioinformatics services SSP and miRInform™ workflows

  • Data summarization (if necessary)
  • Normalization by VSN
  • Calculation of QC metrics
  • Statistical analysis by one-way or multi-way ANOVA
  • Generation of reports and graphs

Custom workflows:

Many projects require custom workflows specific to the information available and deliverables required. Contact Asuragen for information on any of these workflows or other services not listed here:

  • Custom array processing workflows, including alternative target preparation or labeling protocols
  • Biomarker signature or classifier development, validation, equivalence testing, or CLIA implementation
  • Pathway analysis by Gene Set Enrichment Analysis (GSEA)
  • microRNA target prediction and associated mRNA pathway analysis