[rghan]

Can anyone with Agilent 2200 TapeStation experience comment on how it interprets quality for plant RNA? (This would be a quality check prior to library creation) I just sent two plates to a sequencing center and am seeing some serious degradation in my RNA, based on RIN value, that I did not see when running the tests internally at my institution. At least to me, the instrument does not call the rRNA peaks correctly or in a consistent manner from one sample to the next, compared to bioanalyzer 2100 or biorad's experion (I use both internally).

cheers-
ryan

[elbe]

PLease take a look at AATI Fragment Analyzer

http://www.aati-de.com/instruments/fragment_analyzer/index.html

[Expert]

Can anyone with Agilent 2200 TapeStation experience comment on how it interprets quality for plant RNA? (This would be a quality check prior to library creation) I just sent two plates to a sequencing center and am seeing some serious degradation in my RNA, based on RIN value, that I did not see when running the tests internally at my institution. At least to me, the instrument does not call the rRNA peaks correctly or in a consistent manner from one sample to the next, compared to bioanalyzer 2100 or biorad's experion (I use both internally).

cheers-
ryan

Hi Ryan,
I think my answer is very late but hopefuly it will help our other researcher friends. At the moment the tapestation software doesnt have the functionality to give RINe for plant samples. Its validated and is accurate only for eucaryotic samples.
Cheers, Sara

[northpaw]

I think he jury is in on this one. Illumina evaluated all systems on the market to improve reliability, throughput, and dynamic range of analysis for their workflows. This of course included the TapeStation. Illumina doesn't recommend the TapeStation, they have recommended the BA as you know for years.

Do a google search for the Illumina Automation Partners webpage. Scroll down and you will find the Advanced Analytical Fragment Analyzer (FA).

Illumina R&D has integrated the FA into multiple divisions including Consumables Product Development, Diagnostics, and Oncology. They are even starting to release new sample prep kits with the FA as a recommended QC platform.

The latest was the TruSeq RNA Access kit. They have a tech note for degraded RNA sample analysis that describes how they use custom software settings on the FA to streamline analysis of a new critical QC metric for RNA samples they call DV200.

You can find this in a google search on the Illumina website:

[PDF]Evaluating RNA Quality from FFPE Samples - Illumina
res.illumina.com/documents/.../technotes/technote-truseq-rna-access.pdf
Technical Note: RNA Sequencing. Introduction. The TruSeq® RNA Access Kit provides an exon-capture, RNA-Seq approach for difficult samples such as RNA …

If you work with FFPE or any samples prone to degradation by digestive enzymes, you should definitely check out this new kit from Illumina. Its pretty amazing.

[ddpuskas]

LabChip GX Touch - PerkinElmer

You should consider PerkinElmer's new instrument for QC...LabChip GX Touch. There is a low-throughput version 1-24 samples and high-throughput version up to 384.

I demo'd one, seems fine. It's simpler to use than a bioanalyzer, so nothing special. My big issue is the pricing. I'm getting told it costs as follows:

List: 49,000 USD
Negotiated: 34,000 USD

From my sources I have the following:
List: 43,000 USD
Negotiated: 25-30,000 USD

What alternatives are there to the Agilent Bioanalyzer and Tape Station? They can't be the only game in town.

[floem7]

Recently we have presentation of Fragment Analyser.

It's big advantage is lack of pricey chips, one just have to buy some chemicals. Another one plus is great scalability.

Although, as it depends on bottle with appropriate gel you have to replace it if you plan to reslove other molecules (DNA vs RNA). So it's best if you have many samples of one type (DNA/RNA) to measure.
During presentation we resolved marker made from digested pUC, I was quite suprised to see that fragment sizing was a little different from provided by pUC marker flyer (but relative band sizes were ok). For each measurement one have to use internal marker (small fragment and big fragment) and measurement is somehow compromised if molecules in sample have similar size (this two-band marker and sample is resolved in one capillary).

It, also can't resolve proteins.

Nevertheless I regret I can't afford it.