[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.

[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.

[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.

[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

[elbe]

PLease take a look at AATI Fragment Analyzer

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

[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

[winegard]

We are considering a LabchipGX (Caliper).
Anyone with experience running it in the lab? Good and bad issues?

Hi Jakob,

We have a Caliper GXII but have not used it to it's full potential. It's actually quite a good machine - the one limitation of it (that caused us to stop using it for a while) is that it cannot handle gDNA. In fact, if there is gDNA in your sample at all, it will clog the sipper chip, so you have to remove gDNA before running samples which was our problem.

That being said - I'm considering bringing it out of retirement as we are now doing a lot of NGS work and it will be very handy for looking at our libraries etc...

Neil

[K.Hopkins]

We recently had a TapeStaion on demo and it is quicker to get running than the bioanalyzer. The problem we had is that the High Sensitivity kits only size up to 1000bp, above this and the data is out of reach, and it is not uncommon for our libraries to be round this figure.

We were told the gDNA kit would work on these libraries. Has anyone tried this kit? as I have a few concerns about the sensitivity of it.

[Smriti]

Hi Surfnturf,

We have observed lot of variability in sizing for genomic DNA using AATI gDNA kit. They claim its only for checking intactness of DNA and not accurate sizing. Which kit do u guys use for sizing on AATI instrument. Lower bp kit seems to work better. But we are more worried for higher bps as NGS market is moving towards higher fragments.

Any suggestions?

[surfnturf]

Would look to the tape station if using less than 6 samples a day on a regular basis, but once a lane has been punctured the rest of the tape has limited half life, and the cost per sample is high with the tape and special tips for sample loading. Considering the fragment analyzer by advanced analytical since running 12+ samples a day and may ramp that up further. Plated based , CE with 12 or 96 cap setup, high sensitivity (50 pg/ul for pre NGS fragments), resolves fragments up to 20 kb, analyzes gDNA, and has low cost per sample. Writing it into a grant, hope to get one ASAP.

[JakobHedegaard]

We are considering a LabchipGX (Caliper).
Anyone with experience running it in the lab? Good and bad issues?

[QSU88]

We bought one. it's been used for a month, good for quick QC assessment, extension run gives more chance to run sample longer without using new sample.

[TonyBrooks]

We had a very quick play on the Shimadzu and were suitably impressed. It's no way near as sensitive as the Bioanalyser, but for QC steps where there is lots of material (>10ng/µL) it looks decent enough.
The best thing about it is you can load a 96 well plate of samples and walk away which is just what we need for high throughput protocols. A whole plate takes a few hours as there are four capillaries. It saves having to spend a day running Bioanalyser chips which is currently a big bottleneck for us (as well as being a bit soul destroying when needing to QC a few hundred samples). Each sample costs about 30p to run so it's also much cheaper.
Unfortunately, we're feeling the squeeze at the moment, otherwise we would have definitely considered buying one.

[MrGuy]

Ok, so we have the following...

BioRad Experion
Shimadzu MultiNA
Qiagen Qiaxcel
Caliper Labchip

None of them seem to get down to the same level of sensitivity (2 or 3 orders of magnitude) as the Agilent equipment. Most of the alternatives seem to focus on PCR-gel replacement.

http://seqanswers.com/forums/showthread.php?t=15098

[winegard]

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

There's the BioRad Experion.