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Small RNA Regulates Gene Expression

Through Several Mechanisms

 

Small noncoding RNAs are typically only ~18–40 nucleotides in length, but their effects on cellular processes are profound. Small RNAs have been shown to play critical roles in developmental timing, cell fate, tumor progression, and neurogenesis.

Animals, plants, and fungi contain several distinct classes of small RNAs, including:

  • microRNA (miRNA)
  • short interfering RNA (siRNA)
  • piwi-interacting RNA (piRNA)
  • repeat associated small interfering RNA (rasiRNA)

Small RNA Analysis With the 5500xl Genetic Analyzer

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Overview of SOLiD® Total RNA-Seq Kit Workflow

The SOLiD® Small RNA Solution is a robust method for hypothesis-neutral, whole genome analysis of expression patterns that enables you to discover novel RNA without the probe bias of microarrays. Using the SOLiD® Total RNA-Seq Kit, you can convert total RNA into a library in a single day. This simplified protocol reduces experimental variability and improves the detection of biologically relevant changes.

The SOLiD® Total RNA-Seq kit is a single kit for the construction of libraries either for small RNA or whole transcriptome analysis.

Together, the SOLiD® Total RNA-Seq Kit and the ultra–high-throughput 5500xl Genetic Analyzer:

  • Conserve strand specificity of cDNA—allowing you to know exactly which strand a particular small RNA originated from
  • Offer better sensitivity—high number of mapped reads coupled with the accuracy of exact call chemistry (ECC) give confidence in detecting rare and low-abundance small RNAs
  • Offer versatile inputs—analyze small RNAs from a variety of sample types, including quality compromised samples, such as RNA from FFPE tissue, starting with as little as 5 ng   Learn More
  • Detect novel RNAs—facilitate detection of unmapped small RNAs and isoforms
  • Allow multiplexing—sequence multiple small RNA libraries simultaneously in a single lane, helping to reduce the cost of analysis per sample  

Step-by-Step Guide to Small RNA Analysis

Determine the level of sensitivity you need and the number of samples you want to analyze. Internal research conducted at Applied Biosystems suggests 10 million mappable sequences are needed for profiling known miRNAs in humans. Other organisms with similar sized genomes are expected to require a similar number of mappable sequences. It is not known at this time how many mappable sequences may be necessary to confidently discover new species of small RNAs.

Learn More:

Ordering Information

Sku Name Size Price Qty
AM1560 mirVana™ miRNA Isolation Kit, with phenol 40 preps USD 288.00
AM1556 mirVana™ PARIS™ RNA and Native Protein Purification Kit 40 preps USD 310.00
AM1975 RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE 40 preps USD 310.00
K157001 PureLink® miRNA Isolation Kit 25 preps USD 194.00

Ordering Information

Sku Name Size Price Qty
4445374 SOLiD™ Total RNA-Seq Kit 12 preps USD 1,566.00
4427046 SOLiD™ RNA Barcoding Kit, Module 1-16 16 libraries USD 2,325.00
4453189 SOLiD™ RNA Barcoding Kit, Module 17-32 16 libraries USD 2,325.00
4453191 SOLiD™ RNA Barcoding Kit, Module 33-48 16 libraries USD 2,325.00
4456501 SOLiD™ RNA Barcoding Kit, Module 49-64 48 libraries USD 2,325.00
4456502 SOLiD™ RNA Barcoding Kit, Module 65-80 48 libraries USD 2,325.00
4456503 SOLiD™ RNA Barcoding Kit, Module 81-96 48 libraries USD 2,325.00
4461565 SOLiD™ RNA Barcoding Kit, Module 1-48 144 libraries USD 6,200.00
4461566 SOLiD™ RNA Barcoding Kit, Module 49-96 144 libraries USD 6,200.00
4461567 SOLiD™ RNA Barcoding Kit, Module 1-96 288 libraries USD 10,340.00
4453093 SOLiD™ EZ Bead™ E10 System Consumables 4 packs USD 2,645.00
4453094 SOLiD™ EZ Bead™ E20 System Consumables 4 pack USD 3,340.00
4453095 SOLiD™ EZ Bead™ E80 System Consumables 4 pack USD 3,915.00
4465571 SOLiD™ EZ Bead™ E120 System Consumables 4 packs USD 5,940.00
4452720 SOLiD™ EZ Bead™ Emulsifier E10 Reagents Kit 1 kit USD 96.75
4452721 SOLiD™ EZ Bead™ Emulsifier E20 Reagents Kit 1 kit USD 184.00
4452722 SOLiD™ EZ Bead™ Emulsifier E80 Reagents Kit 1 kit USD 504.00
4465555 SOLiD™ EZ Bead™ Emulsifier E120 Reagents Kit 1 each USD 790.00
4453065 SOLiD™ EZ Bead™ Emulsifier E10 Accessories Kit 1 kit USD 102.00
4453076 SOLiD™ EZ Bead™ Emulsifier E20 Accessories Kit 1 kit USD 102.00
4453070 SOLiD™ EZ Bead™ Emulsifier E80 Accessories Kit 1 kit USD 112.00
4465569 SOLiD™ EZ Bead™ Emulsifier E120 Accessories Kit 1 each USD 112.00
4457185 SOLiD™ EZ Bead™ Emulsifier Oil Pack Kit 1 kit USD 81.50
4453071 SOLiD™ EZ Bead™ Amplifier E10 Accessories Kit 4 packs USD 112.00
4453077 SOLiD™ EZ Bead™ Amplifier E20 Accessories Kit 4 packs USD 112.00
4453072 SOLiD™ EZ Bead™ Amplifier E80 Accessories Kit 4 packs USD 143.00
4452723 SOLiD™ EZ Bead™ Enricher E10 Reagent Kit 1 kit USD 102.00
4452724 SOLiD™ EZ Bead™ Enricher E20 Reagent Kit 1 kit USD 189.00
4452725 SOLiD™ EZ Bead™ Enricher E80 Reagent Kit 1 kit USD 534.00
4465564 SOLiD™ EZ Bead™ Enricher E120 Reagents Kit 1 each USD 1,068.00
4444140 SOLiD™ EZ Bead™ Enricher Buffer Reagent Kit 1 kit USD 117.00
4453073 SOLiD™ EZ Bead™ Enricher Accessories Kit 1 kit USD 204.00

Learn More:

User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community.  Access is through the 5500 Series User Hub.  Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub.

Ordering Information

Sku Name Size Price Qty
4460730 5500xl Genetic Analyzer 1 instrument Request a Quote  
4452865 5500 Genetic Analyzer 1 instrument Request a Quote  
4461826 SOLiD™ 6-Lane FlowChip 1 kit USD 678.00
4463011 SOLiD™ FWD1 SP Kit 1 kit USD 167.00
4463012 SOLiD™ FWD2 SP Kit 1 kit USD 167.00
4463019 SOLiD™ REV1 (RNA) SP Kit 1 kit USD 209.00
4463020 SOLiD™ REV1 (DNA) SP Kit 1 kit USD 209.00
4463013 SOLiD™ Small RNA SP Kit 1 kit USD 167.00
4463030 SOLiD™ REV SR Kit, Double 1 kit USD 3,225.00
4463032 SOLiD™ FWD ECC Module, Double 1 kit USD 1,146.00
4461840 SOLiD™ Run Cycle Buffer Kit, Double 1 kit USD 642.00
4459193 SOLiD™ FWD Buffer, Double 1 kit USD 78.50
4463027 SOLiD™ REV Buffer, Double 1 kit USD 78.50
4458935 SOLiD™ Buffer D, Double 1 kit USD 78.50

The tools you need for each step in the Small RNA data analysis workflow:

 
Data Analysis Step Applied Biosystems Software 3rd-Party Software***
1. Align reads to reference in color space
2. Generate quality metrics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
 
3. Generate sequencing and alignment statistics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
4. Count and quanitate tags
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
5. Translate color space to base space  
6. Visualize in context of annotation
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
7. Convert to SRF for publishing    
*** Need XSQ --> csfasta/qual converter

Learn more

Ordering Information

Sku Name Size Price Qty
4440418 Custom TaqMan® Small RNA Assay 75 reactions USD 263.00
4398987 Custom TaqMan® Small RNA Assay 150 reactions USD 304.00
4398988 Custom TaqMan® Small RNA Assay 750 reactions USD 716.00
4398989 Custom TaqMan® Small RNA Assay 2900 reactions USD 1,540.00
4427975 TaqMan® MicroRNA Assay 150 reactions USD 173.00
4440885 TaqMan® MicroRNA Assay 75 reactions USD 214.00
4440886 TaqMan® MicroRNA Assay 150 reactions USD 280.00
4440887 TaqMan® MicroRNA Assay 750 reactions USD 652.00
4440888 TaqMan® MicroRNA Assay 2900 reactions USD 1,528.00

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.