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Old 05-23-2011, 08:52 AM   #1
Deli Çoban
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Arrow initial amount of total RNA or enriched small rna for small rna seq

Hi everyone,

We are planing to small RNA sequencing using Illumina Genome Analyzer (Solexa), my question is how much the initial amount of total RNA should be in general ? or enriched small rna?

many thanks
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Old 05-29-2011, 11:43 PM   #2
ishmael
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Which species? And how about the length restriction?
For what we did for human and other mammals at the length range less than 40nt, the most of final results were known miRNAs, about occupied 80~90% or even more. let-7 families were the highest abundant families.
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Old 05-30-2011, 01:35 PM   #3
Deli Çoban
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First, thanks ishmael for your response

We want to sequence two endemic fish species whose genome are not sequenced and annotated in database. Our study mainly covers the microRNA sequencing and their proposed relatively lenght is between 18-30 nt. My question is how much (ng or ug) the initial RNA quantity (small enriched rna or total rna) should be?

thanks...
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Old 05-31-2011, 10:39 PM   #4
ishmael
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Quote:
Originally Posted by Deli Çoban View Post
First, thanks ishmael for your response

We want to sequence two endemic fish species whose genome are not sequenced and annotated in database. Our study mainly covers the microRNA sequencing and their proposed relatively lenght is between 18-30 nt. My question is how much (ng or ug) the initial RNA quantity (small enriched rna or total rna) should be?

thanks...
Sorry, I forget the topic is about library preparation
Guys in our wet lab said it is hard to say the mass of total RNAs, may be 1mg? They just followed the protocols. Sometimes only when the sequencing finished then you know if the exaction is messed up or not. In the beginning, some sequencing batches of our samples were full of adaptor sequences only, useless .
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Old 06-04-2011, 04:47 PM   #5
Deli Çoban
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Quote:
Originally Posted by ishmael View Post
Sorry, I forget the topic is about library preparation
Guys in our wet lab said it is hard to say the mass of total RNAs, may be 1mg? They just followed the protocols. Sometimes only when the sequencing finished then you know if the exaction is messed up or not. In the beginning, some sequencing batches of our samples were full of adaptor sequences only, useless .
Hi, ishmael

During the library preparation, approximately 1 ug (< 50 pb) enriched small RNA sould be suffecient to get proper sequences for illumnia hiseq2000, according to friends who runs this machine routinely. But, now I embark on collecting part of article about my subject. And, I am planing to list this information here.

kindly...
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