Editing BioMicroCenter:RNA LIB (section)

== [http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/Next_Gen_Sequencing_Kits/Total_RNA-Seq/Pico_Input_Total_RNA_Seq_Illumina Clontech SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian -- aka Clontech ZapR] == 
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  !Service 
  !Low Input RNA Depletion Library Prep
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  |INPUT || Clean Human/Mouse total RNA <BR> DV200>0.5 <BR> >1ng <BR> >10uL where possible
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  |INCLUDED || Initial QC by FemtoPulse <BR> Library preparation <BR> Illumina QC
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  |SUBMISSION || MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 ilabs] <BR> External - [[BioMicroCenter:Forms|form]]
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  |UNIT || Per sample
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For samples with less then 100ng of input and restricted input amounts, our kit of choice is the Clontech SMARTer Stranded Total RNAseq Kit - Pico Input -- or more simply, Clontech ZapR . This kit utilizes the same template switching as the v4 kit but uses random primers on fragmented RNA. The key is the ZapR enzyme which is used post library production to, in a targeted manner, cause breaks in Illumina library molecules that contain rRNA reads. These breaks make the rRNA containing molecules unreadable. This chemistry can be utilized in HTL format as well. <BR><BR>

In analyzing data from this kit, we have observed that the first few nucleotides from many reads appear to have a very high mismatch rate, particularly from low input samples or samples that possibly may not be as clean as desired. We believe this is a results of the template switching and random priming. A 5nt trim from the 5'end of the read can significantly improve data quality.
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