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Old 12-01-2011, 07:48 AM   #1
epibio
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Default New ScriptSeq v2 RNA-Seq Library Prep Kit

The new ScriptSeq™ v2 RNA-Seq Library Preparation Kit from Epicentre is now available. The kit offers several improvements over the original ScriptSeq Kit, including better transcript coverage, lower RNA input requirement, a streamlined procedure, and lower cost. For more information, please see the product page.

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Old 12-19-2011, 08:00 PM   #2
Dario1984
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Are there UCSC Browser tracks of mapped reads anywhere of a whole sample dataset ? In other words, not just a screenshot of one gene, which all the kit manufacturers seem to think is convincing. We're interested in a kit with good 5' to 3' evenness for mRNA-seq. The RNA is from cell lines and is not degraded.
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Old 12-20-2011, 10:28 AM   #3
epibio
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Not yet, but we're working on it. At present, the other data we have is a 600-gene coverage plot that I can send you.
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Old 12-20-2011, 10:49 AM   #4
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I would also be very interested to see your 600-gene coverage plot. Thanks
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Old 12-20-2011, 01:46 PM   #5
epibio
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This is the 600-gene coverage, single-end sequencing reads from the 5' end so there is an expected drop in coverage at the 3' end. I'll post the UCSC browser plots when they are available.

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Old 03-16-2012, 05:33 AM   #6
censinis
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Based on manufacturer's suggestion, the ScriptSeq v2 RNA-Seq Lib Prep kit is well suited to work with 500 pg to 50 ng of either ribodepleted or poly(A)+ RNA. I am wondering if it is possible to start with totRNA of bacterial origin and, in that case, how much totRNA has to be reverse transcribed.
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Old 03-16-2012, 05:57 AM   #7
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Do you have data of how this kit perform with other mainstream kits? truseq RNA will be nice if you have a comparison
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Old 03-16-2012, 06:47 AM   #8
epibio
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Quote:
Originally Posted by censinis View Post
Based on manufacturer's suggestion, the ScriptSeq v2 RNA-Seq Lib Prep kit is well suited to work with 500 pg to 50 ng of either ribodepleted or poly(A)+ RNA. I am wondering if it is possible to start with totRNA of bacterial origin and, in that case, how much totRNA has to be reverse transcribed.
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S
In theory, you could use the kit with total RNA at the higher end of the input range. However, since 95-99% of your reads will map to ribosomal RNA, it would not be a good idea.
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Old 03-19-2012, 12:38 AM   #9
censinis
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Of course. Nevertheless, I did experience not exciting results in ribodepleting meningococcal rRNA from pretty good totRNA preps (RIN >9), with approx 60% of rRNA related reads still left after Ribo-Zero (Gram-) treatment as judged by evaluating HiSeq 2000 output data. Because the enormous mole of sequences we can raise in a single HiSeq lane (approx 30Gb), we can still expect enough space to approach the expected bacterial transcriptome complexity. Please let me know if you have any any alternative suggestion.
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S
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Old 04-04-2012, 04:37 PM   #10
Jperrott
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Default Using ScriptSeq V2 on ~1ng total RNA

I was wondering how well would the ScriptSeq V2 kit work on roughly 1ng total RNA? I ask this because performing a Ribominus or PolyA selection on such a small amount of total RNA seems risky. I realize that we would most definetly get rRNA reads mapping, but even with a 40% mapping of mRNA fragments, this would be ideal for my particular application.
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Old 04-06-2012, 06:05 AM   #11
epibio
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The ScriptSeq v2 kit will perform well with 1 ng total RNA; as you expect, the majority of your reads would be ribosomal RNA.
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