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Old 10-11-2011, 10:36 AM   #1
epibio
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Default New Ribo-Zero Gold Kit (Human/Mouse/Rat)

The Ribo-Zero Gold Kit (Human/Mouse/Rat) is an enhanced version of Epicentre's popular Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat). The Ribo-Zero Gold Kit removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 g of human, mouse, or rat total RNA preparations for RNA-Seq and other applications. For more information, please see the product page.
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Old 11-30-2011, 07:29 AM   #2
otmagnus
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Hello
Im interested in using Ribo-Zero in conjunction with the ScriptSeq prep for Total RNA-Seq. Do the protocols support capture and sequencing of microRNA (<30nt) or would I be limited to larger ncRNA (lincRNA etc)?
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Old 11-30-2011, 01:31 PM   #3
epibio
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The Ribo-Zero method will allow for purification of microRNA, as long you use a suitable clean-up method at the end. The ScriptSeq kit is not designed for microRNA library prep; instead, we recommend using our ScriptMiner small RNA-seq kit.
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Old 12-01-2011, 12:53 AM   #4
otmagnus
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yes, I realize that you have specific preps for microRNA like Illumina has, but this would call for two separate preparations for the same samples(s). I just wanted to know that even though the ScriptSeq is not designed for microRNA, whether the microRNA could be included, either by the standard workflow or by some modification. It seems the small/micro RNA would presumably be lost in the ScriptSeq workflow during purification steps, but if there is an alternative purification method perhaps it could be included?
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Old 12-01-2011, 05:40 AM   #5
epibio
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The main issue with microRNA and a ScriptSeq workflow is that these small RNAs are significantly under-represented in the cDNA, since it is produced by a random-primed method. It will work fine for long ncRNAs but not for microRNA.
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Old 12-07-2011, 06:35 AM   #6
Oliviervg
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Hi,

- In the profiles of RNA-seq libraries prepared after treatment with the Ribo-Zero and Ribo-Zero Gold Kits (Fig 1), what do you mean by "genomic", "Aligning exomic" and "partial exomic"

- Does the yield differ between this two kit ?

Thank you
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Old 12-07-2011, 09:25 AM   #7
epibio
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The yields are similar for the standard Ribo-Zero and the Ribo-Zero Gold kits, i.e., ranging from 3% to 10% of input amount, depending on the type of total RNA sample.

The mapping was done using Genomatix RegionMiner. The default parameters are as follows:

Quote:
In case the region classification has been checked, a table with the number of regions contained in genomic elements is given. Each input region is classified either as

exonic, complete or
exonic, partial (i.e. overlapping with an exon) or
intronic, complete or
intergenic region
In the figure legend, what is marked as intronic should be "complete intronic", and the "genomic" should be the same as "intergenic". However, I'll confirm with the folks who did the analysis and let you know.
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Last edited by epibio; 12-07-2011 at 09:32 AM. Reason: Added info
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Old 08-01-2014, 12:35 PM   #8
shrutimish@gmail.com
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Hi, I recently heard that Ribo Gold introduces a bias while removing the rRNA, is it true? I was suggested not to use Illumina Truseq stranded total RNA protocol because of this.
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