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Old 03-05-2015, 11:07 AM   #1
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Location: New Haven, CT

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Default Library Prep from Limited RNA Samples

I am new to the field of Library Preparation and RNA-Seq in general, and have some questions about the best options for performing transcriptome analyses on my samples.

I have limited amounts RNA (50-80ng total per sample, at 2-4ng/uL) prepared from my samples of interest, and I am looking to prepare Libraries for sequencing with the NextSeq 500 sequencer.

As far as I can tell, my RNA quantities are too low for traditional library preparation, leaving me with a choice between RNA amplification kits or alternative library preparation kits such as the TruSeq RNA Access Kit (which isolates RNA coding regions for sequencing). Is there a clear advantage to choosing one of these strategies over the other? Are there alternative strategies/kits that I am not aware of that might work bettter? I would greatly appreciate any help that you can provide.
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Old 03-05-2015, 12:43 PM   #2
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There are a number of low input RNA kits that can work with your input amounts. See:
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Old 03-06-2015, 01:40 AM   #3
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if you want to do it cheap and without kits you can use our Smart-seq2 protocol. It works only for mRNA and gives a non-stranded library. See PMID: 24056875; 24385147. Its optimized for single cells but works also with 1-10 ng tot RNA.

If you have enough RNA (and money!), want a stranded library and all the RNAs (also the non-polyA+) you should use the SMARTer Stranded Total RNA Sample Prep Kit (Clontech).

If you want to do only tag-seq (seq only the 5or the 3of the transcripts) you should use either the CEL-seq (PMID: 22939981;24531970) or STRT (PMID: 24363023; 21543516)methods.
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