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Forum: Sample Prep / Library Generation 01-21-2014, 05:08 AM
Replies: 4
Views: 2,431
Posted By dottomarco
What is your esperience with the Nextera Exome...

What is your esperience with the Nextera Exome kit so far?
Are you getting the same % of reads on targett? I am mostly interested about the coverage that I can get using these libraries compared to...
Forum: Sample Prep / Library Generation 10-23-2013, 08:28 AM
Replies: 5
Views: 5,035
Posted By dottomarco
Exome enrichment, How does Nextera Exome Enrichment compares to TrueseqNimbleAgilent?

I have been trying all the different exome enrichment kits available during the last years.
I am now wondering what the real performance of the new Nextera Rapid Exome enrichment kit (37 or 62 Mb...
Forum: Illumina/Solexa 03-09-2012, 06:39 AM
Replies: 12
Views: 3,868
Posted By dottomarco
Hi, we are now evaluating the SPRIworks System in...

Hi, we are now evaluating the SPRIworks System in order to do the library prep for our 454 and for HiSeq. I read your posts about the issues you faced with the system. We will be sequencing mostly...
Forum: Vendor Forum 03-09-2012, 06:01 AM
Replies: 5
Views: 4,381
Posted By dottomarco
Any news about the 454 PLUS libraries ? We are...

Any news about the 454 PLUS libraries ?
We are planning to use the SPRIworks System for Illumina HiSeq and 454+ library prep. Can anyone give some feedback about the performance of the sequencing...
Forum: Service Providers 08-05-2011, 12:47 AM
Replies: 162
Views: 155,200
Posted By dottomarco
Dear scalabrin...

Dear scalabrin <http://seqanswers.com/forums/member.php?u=4018>,

I am sorry for the misunderstanding and I thank you for pointing this out.
I din't intend to damage anyone; BMR Genomics is a...
Forum: Service Providers 08-03-2011, 02:26 AM
Replies: 162
Views: 155,200
Posted By dottomarco
BMR Genomics, Italian leader for Sanger and NGS...

BMR Genomics, Italian leader for Sanger and NGS services now offers sequencing on
454 FLX
Illumina HiSeq 1000
SOLiD 5500 XL

and Bioinformatics Analysis services on NGS data.

For...
Forum: General 07-28-2011, 05:50 AM
Replies: 10
Views: 2,985
Posted By dottomarco
Can someone provide links or pdfs of any other...

Can someone provide links or pdfs of any other paper were the 2 or 3 technologies are compared especially regarding error rates, false <0 and <0, etc. ??
Looking at GA and SOLiD 2 is not that useful...
Forum: Illumina/Solexa 07-27-2011, 02:15 AM
Replies: 0
Views: 2,266
Posted By dottomarco
Mate-Pair Illumina library problems

Hi, I am about to start a resequencing project on the HiSeq 1000 searching for rearrangements in a bacterial genome.
This is the 1st time I am going to use the mate pair approach, so I am wondering...
Forum: Sample Prep / Library Generation 06-23-2011, 07:48 AM
Replies: 23
Views: 12,958
Posted By dottomarco
Talking I guess it is with the V2 reagents right...

I guess it is with the V2 reagents right NextGenSeq?? TrueSeq V3 should produce 375 millions paired end reads oer lane.. So now it should be possible to get 6 exomes per lane with a pretty decent...
Forum: 454 Pyrosequencing 04-27-2011, 01:25 AM
Replies: 28
Views: 10,578
Posted By dottomarco
So are you saying the ION EXPRESS (new automating...

So are you saying the ION EXPRESS (new automating machine for the ION torrent) can be used for the 454 library prep ? The REM is supposed to be used for the automation of the enrichment part of the...
Forum: Sample Prep / Library Generation 01-25-2011, 01:08 AM
Replies: 23
Views: 12,958
Posted By dottomarco
the new SureSelect targets 50Mb, why would you...

the new SureSelect targets 50Mb, why would you use the old version (38Mb)?

Sequence enrichment usually yield 60/70% of reads on target... and just 75% of these will be HQ... so you end up with ...
Forum: 454 Pyrosequencing 10-06-2010, 01:37 AM
Replies: 12
Views: 6,314
Posted By dottomarco
yes, this was a test to try the "multiplexing"...

yes, this was a test to try the "multiplexing" process in general... for small targets that's obviously not necessary.

Any idea how the seq enrichment perform with Sureselect for small targets...
Forum: 454 Pyrosequencing 10-05-2010, 05:35 AM
Replies: 12
Views: 6,314
Posted By dottomarco
We tried it. got good results about pretty must...

We tried it. got good results about pretty must everything apart from % of reads on target (which is the actual important thing). we tested different tiling (2x, 5x, 10x and 2x multiplexing 2 samples...
Forum: 454 Pyrosequencing 04-28-2010, 11:12 AM
Replies: 14
Views: 10,241
Posted By dottomarco
Thanks a lot AKroxy ! Roche reps around the word...

Thanks a lot AKroxy ! Roche reps around the word must have different conception of "confidential" information.
At list now we know that the adaptors are the same as the "standard" adaptors except...
Forum: 454 Pyrosequencing 04-23-2010, 07:58 AM
Replies: 14
Views: 10,241
Posted By dottomarco
We need to amplify the rapid library and I really...

We need to amplify the rapid library and I really do not understand the point of not let the users know what the adaptor's sequences are?
Any idea on how to design a couple of primers to amplify the...
Forum: 454 Pyrosequencing 04-23-2010, 01:59 AM
Replies: 14
Views: 10,241
Posted By dottomarco
Hy ulz_peter. I have that exact pdf, but it is...

Hy ulz_peter. I have that exact pdf, but it is the TECHNICALM BULLETIN for the amplicon protocol titanium.
I am sewarching for the exact same correspondent for the RAPID LIBRARIES.
The picture of...
Forum: 454 Pyrosequencing 04-23-2010, 12:08 AM
Replies: 14
Views: 10,241
Posted By dottomarco
RAPID Libraries adaptor+key sequences

I was wondering if any of you know what the adaptors A and B sequences are (+ key sequence).
Even better if you can also provide the MID sequences of the kit that is shipped by Roche for the rapid...
Forum: Genomic Resequencing 04-14-2010, 07:21 AM
Replies: 4
Views: 3,452
Posted By dottomarco
MYcroarray.com are starting to provide liquid...

MYcroarray.com are starting to provide liquid enrichment altough they target few Mbs, and they require few ngs of libraries.
No idea about how their probes work for actual enrichment. I am testing...
Forum: 454 Pyrosequencing 03-11-2010, 09:51 AM
Replies: 3
Views: 2,359
Posted By dottomarco
They do not have a sequence enrichment product...

They do not have a sequence enrichment product (array) out yet. What we are trying to do is testing their arrays to see if they could be usable (and most interestingly for $ , REUSABLE) for seq...
Forum: 454 Pyrosequencing 02-19-2010, 09:14 AM
Replies: 4
Views: 5,954
Posted By dottomarco
This is based on the old library protocol right?...

This is based on the old library protocol right? Now the new rapid library protocol solved a lot of issues.. but it wold be interesting to apply the 96 parallelization idea of the paper to the new...
Forum: 454 Pyrosequencing 02-19-2010, 06:32 AM
Replies: 12
Views: 6,314
Posted By dottomarco
Thanks flxlex for the answer. With the present...

Thanks flxlex for the answer. With the present Nimblegen protocol you use the 454 adapters which are present in the library, to perform a PCR amplification after the enrichment. 1-2 years ago...
Forum: Genomic Resequencing 02-19-2010, 06:04 AM
Replies: 28
Views: 12,634
Posted By dottomarco
@ NGSfan : What sequencer did you use? Illumina...

@ NGSfan : What sequencer did you use? Illumina GA II?
I am interested in using Agilent's SureSelect for sequence enrichment to get the targets to sequence with a 454 FLX. Do you think using a long...
Forum: 454 Pyrosequencing 02-18-2010, 11:39 PM
Replies: 12
Views: 6,314
Posted By dottomarco
Target Sequence Enrichment 454

Hi everybody !
I am having a huge issue with the sequence enrichment for 454. My interest (and with me I think many of you folks) is to target small portions of the human genome and sequence many...
Forum: 454 Pyrosequencing 02-10-2010, 08:04 AM
Replies: 28
Views: 10,578
Posted By dottomarco
I am interested in the REM too. It seems it is...

I am interested in the REM too.
It seems it is going to work for the emPCR part only..why not also the library preparation part?
We have a Biomek FX.. I hope they are going to provide the ready to...
Forum: Service Providers 11-17-2009, 08:55 AM
Replies: 162
Views: 155,200
Posted By dottomarco
italy : BMR GENOMICS has a 454 (just to fill that...

italy : BMR GENOMICS has a 454 (just to fill that gap)

thanks
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