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Updated: Jun 14, 2026
High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs
Published on: August 3, 2011
Optimizing protocols for microRNA profiling of infant and toddler stool
David A Armstrong1,2, Shannon M Soucy3,4,5, Meghan E Muse6
1Department of Dermatology, Dartmouth Health, Lebanon, NH, USA.
Abstract:
Despite growing interest in profiling microRNAs (miRNAs) in infant and toddler stool, no studies have compared protocols for preserving and extracting miRNAs from this specimen type.
Abstract:
Three commercially available kits and four preservation methods were compared for their ability to yield high quality RNA from children <2 years of age (infant/toddler).
Abstract:
Of the three RNA extraction kits compared, Zymo BIOMICs yielded the highest RNA Quality Number (RQN) (median (range) RQN 9.4 (5.7-10.0)). Of the four preservation methods tested, RNAlater and Zymo DNA/RNA Shield Faecal Collection Tubes yielded the highest two RQNs (median (range) RQN 9.8 (5.7-10.0) and 9.4 (5.4-10.0), respectively), which did not differ from each other (p = 0.47). Subsequently, miRNA-seq was used to compare miRNA profiles for RNA extracted using the Zymo BIOMICs kit from paired aliquots of the same stool sample (n = 4 infant donors) collected into RNAlater and Zymo DNA/RNA Shield Faecal Collection Tubes. The percentage of reads classified as human and the percentage of human reads aligning to miRBase did not differ for samples collected in RNAlater versus Zymo Shield (p = 0.12 and p = 0.86, respectively). Furthermore, after multiple testing correction, normalized miRNA counts did not differ between the two preservatives for any of the 42 human miRNAs detected across the eight samples (pFDR ≥ 0.05).
Abstract:
Collecting stool from infants and toddlers <2 years of age in either RNAlater or Zymo DNA/RNA Shield Faecal Collection Tubes, when paired with RNA extraction using the Zymo BIOMICs extraction kit, yielded high-quality RNA with similar human miRNA profiles.
Insights
This study compared RNA preservation and extraction methods for infant stool, finding Zymo BIOMICs kit with RNAlater or Zymo DNA/RNA Shield tubes yields high-quality RNA and similar microRNA profiles. These methods are suitable for infant microRNA profiling.
Area of Science:
- Biochemistry
- Molecular Biology
- Pediatric Research
Background:
- MicroRNA (miRNA) profiling in infant and toddler stool is gaining interest.
- No prior studies have compared protocols for preserving and extracting miRNAs from this specific sample type.
Purpose of the Study:
- To compare the efficacy of different commercial kits and preservation methods for RNA extraction from infant/toddler stool.
- To determine the optimal protocol for high-quality RNA and reliable miRNA profiling in young children.
Main Methods:
- Evaluated three commercial RNA extraction kits and four preservation methods using stool from children under two years old.
- Assessed RNA quality using RNA Quality Number (RQN).
- Performed miRNA sequencing (miRNA-seq) to compare miRNA profiles from the best-performing preservation methods.
Main Results:
- The Zymo BIOMICs kit yielded the highest RNA Quality Number (RQN).
- RNAlater and Zymo DNA/RNA Shield Faecal Collection Tubes provided the highest RQNs and did not significantly differ.
- miRNA sequencing revealed no significant differences in human miRNA profiles between RNAlater and Zymo Shield preservation methods.
Conclusions:
- Collecting infant/toddler stool in RNAlater or Zymo DNA/RNA Shield tubes, combined with the Zymo BIOMICs extraction kit, produces high-quality RNA.
- These methods result in comparable human miRNA profiles, making them suitable for infant miRNA studies.
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