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Old 09-22-2011, 06:28 AM   #1
Turnerac0987
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Default Bioo Scientific kits

Hey everyone,

I was wondering if anyone had any experience using Bioo Scientific's DNA sequencing kits?
How do they compare with Illumina's TruSeq DNA Sample prep kits? Do the final results look the same or better using one kit or the other?
Also, does anyone know the difference between Bioo Scientific's AIR DNA kits as opposed to their NEXTflex kits? I can't seem to find any differences between them on their website.

Thanks!
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Old 09-22-2011, 03:46 PM   #2
msheldon
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We are very happy with their Nextflex DNA Seq kits and barcodes and have incorporated them into our workflow. We have seen significantly better adapter ligation with Nextflex compared to Truseq. Haven't used AIR, so I can't comment.

I heard from a UC sequencing core that they've released 96 barcodes. Can anyone confirm????
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Old 09-23-2011, 06:01 AM   #3
Turnerac0987
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Thanks for your reply! I'm glad someone has had a good experience with them since they are so much cheaper than Illumina kits.

And yes, I've seen on their website that they have 96 barcodes.

Does anyone else have any insight on the difference between their AIR kits vs their NEXTflex kits?
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Old 09-23-2011, 08:15 AM   #4
Chipper
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NEXTflex barcodes are 6nt, the 96 kit uses 8 bp barcodes. AIR I think is similar to Illuminas 3-primer system? We are happy with the NEXTflex adaptors. They also have a PCR-free system i you are working with more DNA, not sure how it works though.
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Old 09-26-2011, 06:30 AM   #5
Turnerac0987
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Update:
I contacted Bioo Scientific and they were very helpful in explaining the difference between the kits. In case anyone else wants to know, here is what they said.

"The primary difference between the AIR and NEXTflex kits is how the barcode is incorporated. In the AIR kits, the barcode is added during PCR as a third barcoded primer. In the NEXTflex kits, it is added right at the adapter ligation step. This allows you to reduce the amount of PCR cycles required."

I'd still like to hear anyone elses opinions about how Bioo Scientific kits compare to Illumina, but it seems that so far Bioo Scientific kits are a great cheaper alternative.
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Old 09-26-2011, 11:51 PM   #6
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We have found that the NEXTflex kits produce libraries more reliably, especially in the presence of PCR inhibitors. Particularly the ligase and polymerase both seem to be superior to those in TruSeq. So far we have only been using the 48-barcode kit but the 96 has just been released:

http://www.biooscientific.com/Detail...A%20Sequencing
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Old 09-27-2011, 05:26 AM   #7
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We are achieving much better read and quality scores with Nextflex compared to Truseq. In my experience the libraries are more consistent as well.

We use the Nextflex barcodes for genomic and mRNA work. Looking forward to using their 96 set.
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Old 09-27-2011, 05:57 AM   #8
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The specs for the AIR kits say they can be used with as little as 50 ng input material. Has anyone tried these kits using less than that? Any successes or failures? We have samples with only ~10 ng input and are considering Nextera, but AIR is significantly cheaper plus has more barcodes built in.
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Old 10-06-2011, 07:56 AM   #9
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Ok, it looks like the 96 barcodes are confirmed. We're going to get a set today.

http://seqanswers.com/forums/showthr...highlight=bioo

Has anyone used Nextflex with sequence capture ?
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Old 10-07-2011, 08:25 AM   #10
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We are using the Nextflex protocol and barcodes with nimblegen capture.
I think they should be comptible with other capture methods as well, we just decided on the nimblegen route.

Quote:
Originally Posted by msheldon View Post
Ok, it looks like the 96 barcodes are confirmed. We're going to get a set today.

http://seqanswers.com/forums/showthr...highlight=bioo

Has anyone used Nextflex with sequence capture ?
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Old 10-25-2011, 10:06 AM   #11
ssing
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I had horrible experience with the Nextflex kits, but using the same starting material with the TruSeq kits, I got excellent results. I am not sure if this is just me...

Bioo Scientific staff was helpful in helping troubleshoot, though their refund policy is a bit overly stringent.
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Old 10-28-2011, 09:10 PM   #12
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We use about 2-3 Nextflex DNA kits per month and 1 Nextflex Small RNA kit per month for our library preps and send off the sequencing to a core facility in the US. I couldn't be happier with our results. We too notice much better read quality and a greater number of unique reads in our results. I agree they do have excellent technical support.

Just found out that they have modules for each step. We plan on ordering these too.


Quote:
Originally Posted by Turnerac0987 View Post
Hey everyone,

I was wondering if anyone had any experience using Bioo Scientific's DNA sequencing kits?
How do they compare with Illumina's TruSeq DNA Sample prep kits? Do the final results look the same or better using one kit or the other?
Also, does anyone know the difference between Bioo Scientific's AIR DNA kits as opposed to their NEXTflex kits? I can't seem to find any differences between them on their website.

Thanks!
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Old 03-14-2012, 09:26 AM   #13
[email protected]
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Default Strand-specific RNA sequencing using NEXTflex barcoded adapters

Hi everyone,

I was wondering if anyone has used NEXTflex DNA barcodes to generate strand-specific RNA-Seq libraries for sqeuencing on an Illumina GAII or Hi-Seq?

Best wishes,

David
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Old 04-19-2012, 07:08 PM   #14
msheldon
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yes, we are using the nextflex barcodes for strand specific RNA-Seq (uracil method). We are also using their directional RNA-Seq kit which has included directional adapters that can read in the 5'-3' or 3'-5' direction.
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Old 04-30-2012, 11:37 AM   #15
DNautomate
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In case anybody is interested in automation of Bioo kits, an article has recently been published outlining some QC results using these regents with the VERSA Mini NGLP workstation.

http://www.nature.com/app_notes/nmet...f/an8386_1.pdf

Disclosure: I am employed by Aurora Biomed.
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Old 05-08-2012, 02:52 AM   #16
riehle
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Default NEXTflex Chip-Seq Kit and qiagen columns

Hi
I wonder if anybody has experience in replacing the AmpureBeads with Qiagen Columns for lib prep using the NEXTflex Chip-Seq Kit.
Thanxx
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Old 05-08-2012, 07:37 PM   #17
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We are using Bioo's ChIP-Seq kit with beads. I believe you have to use beads because the adapters are long and cannot be removed by columns.
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Old 05-09-2012, 11:55 AM   #18
Devero89
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looks good so far. I will seq the multiplexed lib. that I made with Bioo.
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Old 05-10-2012, 02:44 PM   #19
james hadfield
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Our first four libraries will go on next week, fingers crossed as we'd like to move to 96-plex.
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Old 06-01-2012, 10:52 AM   #20
Devero89
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it worked!!
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