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Search: Posts Made By: MonaE
Forum: Ion Torrent 01-11-2014, 04:43 AM
Replies: 0
Views: 2,389
Posted By MonaE
RNA later and DNA extraction methods

hello Every one. I have two questions:-

1- I would like to use RNA-later media for tissue samples. I would like to know if later I can extract DNA as well.

2- I I would like to use NGS...
Forum: Ion Torrent 11-04-2013, 11:14 AM
Replies: 0
Views: 1,805
Posted By MonaE
Ion one touch

hi,

Does any one knows how to calculate the molarity for Ion one touch 2 use?
Forum: Ion Torrent 10-31-2013, 09:38 AM
Replies: 0
Views: 1,948
Posted By MonaE
Size selection...dropping of DNA quantity

Dear all,

My samples quantities was 246, 184, 112, 133 and 232 ng. I pooled them all and run them in a gel for site selection. Afterward I did purified them using columns. Surprisingly and after...
Forum: Ion Torrent 09-20-2013, 06:57 AM
Replies: 1
Views: 2,535
Posted By MonaE
ION PGM reads

ION PGM is does not read. it tells that the chip does not read at all. What could be the problem? has any one come across similar problem?
Forum: Ion Torrent 09-05-2013, 10:03 AM
Replies: 19
Views: 6,105
Posted By MonaE
For example one of the samples was 52 ng/ul after...

For example one of the samples was 52 ng/ul after PCR then for gene A after purification it changed to be 18,64 ng/ul. another sample was 22 ng/ul after AMPURe became 33,4 ng/ul however when I...
Forum: Ion Torrent 09-05-2013, 09:42 AM
Replies: 19
Views: 6,105
Posted By MonaE
I have measured the samples after the PCR and...

I have measured the samples after the PCR and they had good measurement especially with gene B. After the beads some of them their concentration even increased. The PCR is a custom panel primers that...
Forum: Ion Torrent 09-05-2013, 09:27 AM
Replies: 19
Views: 6,105
Posted By MonaE
I put 5 ul DNA in a total of 20 ul PCR reactions....

I put 5 ul DNA in a total of 20 ul PCR reactions. Before PCR the concentration was between 5,4-8,54 ng/ul . After the beads they really varied.
Forum: Ion Torrent 09-05-2013, 09:14 AM
Replies: 19
Views: 6,105
Posted By MonaE
The DNa product are with a high concentration but...

The DNa product are with a high concentration but I have diluted them to 8ng/Ál, this is according to the protocol requirements. I used 25 cycles with PCR A but 20 cycles for PCR B. The 20 cycles...
Forum: Ion Torrent 09-05-2013, 09:05 AM
Replies: 19
Views: 6,105
Posted By MonaE
Sorry for the table it is a system problem. In...

Sorry for the table it is a system problem. In fact the 17ng/ul is the conc of sample in gene A and the 0.4ng/ul is the con of sample in gene B.

I suspect the beads as well because my first...
Forum: Ion Torrent 09-05-2013, 08:48 AM
Replies: 19
Views: 6,105
Posted By MonaE
Hi, I have measured the concentration of my...

Hi, I have measured the concentration of my samples after AMPure for two different genes and I got variable reading that I do not know how I can pool them.
Gene A Gene B ...
Forum: Ion Torrent 09-05-2013, 08:44 AM
Replies: 19
Views: 6,105
Posted By MonaE
now I have measured the concentration of my...

now I have measured the concentration of my samples after AMPure for two different genes and I got variable reading that I do not know how I can pool them.
Gene A Gene B
ng/μl Quantity in...
Forum: Ion Torrent 08-30-2013, 12:52 AM
Replies: 19
Views: 6,105
Posted By MonaE
Would the number of PCR cycle affects?

Would the number of PCR cycle affects?
Forum: Ion Torrent 08-29-2013, 10:29 AM
Replies: 19
Views: 6,105
Posted By MonaE
Yes, the before and after volume is the same

Yes, the before and after volume is the same
Forum: Ion Torrent 08-29-2013, 04:51 AM
Replies: 19
Views: 6,105
Posted By MonaE
DNA concentration increased

Hi,
My sample concentration after PCR was 52ng/microlitre. After purification with beads it read 63,2 ng/microlitre. Is this normal? usually we lose some DNA after AMpure and this is the first time...
Forum: Ion Torrent 08-26-2013, 03:23 AM
Replies: 6
Views: 7,402
Posted By MonaE
the manuel you put a link to uses 13 pb adaptor...

the manuel you put a link to uses 13 pb adaptor barcode, which is a new one I am not sure that we use in the lab.
Forum: Ion Torrent 08-26-2013, 03:22 AM
Replies: 6
Views: 7,402
Posted By MonaE
In my lab they use two barcodes but the adaptor...

In my lab they use two barcodes but the adaptor is (P1) and there is no (A) adaptor. I do not understand why???? I would like to know if some one uses this
Forum: Sample Prep / Library Generation 07-26-2013, 04:51 AM
Replies: 0
Views: 1,306
Posted By MonaE
Low PCR volume and quantity...affect library prep?

Hi,

I discovered that my I lose between 1-2 micoliter of my PCR material due to evaporation. I do not know why my sample evaporate maybe because I am using only 5 microliter?

in the other hand...
Forum: Ion Torrent 07-22-2013, 07:43 PM
Replies: 6
Views: 7,402
Posted By MonaE
Barcodes and adaptor

hi there,

I have two questions:

1-What is the mechansim with which Ion barcodes and P1 adaptor works?

2- why there is only one adaptor instate of two?
Forum: Ion Torrent 07-20-2013, 01:45 AM
Replies: 3
Views: 4,108
Posted By MonaE
Thank you for your replay. I want to use the gel...

Thank you for your replay. I want to use the gel just to check the (efficiency) of my PCR that is all. I will not cut it or size select. This is becasue when I measure with quibid I get reading that...
Forum: Ion Torrent 07-19-2013, 06:20 PM
Replies: 3
Views: 4,108
Posted By MonaE
Gel run before AMPure

I am using targeted sequencing designed by Qiagen. I would like to perform a gel run for my samples before measuring them by Qubid and AMPure step. The reason I want to do that is because if I...
Forum: Introductions 07-18-2013, 02:57 PM
Replies: 0
Views: 1,225
Posted By MonaE
Amplification-Ion torrent

I am using Ion Torrent. Just in the amplification step the thermocycler had an error. What can I do? should I continue with size selection or I stop and restart from the begining?
Forum: Introductions 05-27-2013, 07:12 AM
Replies: 4
Views: 2,037
Posted By MonaE
Thank you :)

Thank you :)
Forum: Introductions 05-27-2013, 05:45 AM
Replies: 4
Views: 2,037
Posted By MonaE
Thank you for your replay. I was just...

Thank you for your replay.
I was just wondering how do you do these calculations?

I found out that if I used 318 I will get a coverage of 7,84 but should use tow chips as the chip takes 48...
Forum: Introductions 05-27-2013, 03:18 AM
Replies: 4
Views: 2,037
Posted By MonaE
Ion Torrent targeted sequencing

Hello Every one,

I am a new NGS user. I am starting to work on targeted sequencing using Ion Torrent technology.

My targeted gene is BRCA1 and I have about 50 samples. The gene is 112...
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