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Forum: Sample Prep / Library Generation 09-23-2015, 02:44 PM
Replies: 0
Views: 1,278
Posted By Smriti
Barcoding primers for Pac Bio

Hi There,

Has anyone used Pac Bio Barcodes for multiplexing at PCR level. I am trying to test Symmetric barcodes for Pac Bio platform. Did anyone see problems of primer dimers and barcodes not...
Forum: Sample Prep / Library Generation 08-04-2015, 10:10 AM
Replies: 3
Views: 2,185
Posted By Smriti
Hi There, Thanks for your suggestions! I am...

Hi There,

Thanks for your suggestions! I am using Prokaryotic total RNA Pico assay for analyzing quality of RNA extracted from virus, right after extraction. Probably, its low viral loads and I am...
Forum: Sample Prep / Library Generation 08-03-2015, 09:14 AM
Replies: 3
Views: 2,185
Posted By Smriti
Bioanalyzer for viral RNA samples

Hi There,

Has anyone used Bioanalyzer Pico/Nano RNA assays for viral RNA analysis? I am new to the viral genome analysis. I have tried running both the kits with Eukaryotic total RNA assays and...
Forum: Sample Prep / Library Generation 05-28-2015, 01:00 PM
Replies: 2
Views: 1,434
Posted By Smriti
Is Nextera useful for Pac bio in future?

Hi There,

I am working with Nextera workflow. I was wondering if Nextera library prep can be somehow extended to Pac bio platform. My understanding is Nextera insert size is much smaller than what...
Forum: Bioinformatics 02-21-2013, 04:23 PM
Replies: 1
Views: 3,132
Posted By Smriti
Literature on MiSeq data analysis

Hi There,

I am very new to sequencing data analysis and looking for some beginner level literature/book for understanding data. Can anyone suggest me something?

Thanks!
Forum: General 02-15-2013, 02:07 PM
Replies: 2
Views: 5,038
Posted By Smriti
Target resequencing Vs Amplicon sequencing

Hi there,

I am relatively new to the field of DNA sequencing, so asking a basic question here:

What is the difference between Target Resequencing and Amplicon Sequencing? I guess both are done...
Forum: General 02-08-2013, 10:46 AM
Replies: 2
Views: 1,459
Posted By Smriti
Thanks Krobison, For now I'll order...

Thanks Krobison,

For now I'll order Micrococcus from Sigma. I need to test a high G-C content DNA for library preparation. Hope this one will fulfill it.

Bordetella or Rhodobacter, from where...
Forum: General 02-05-2013, 12:11 PM
Replies: 2
Views: 1,459
Posted By Smriti
High GC rich genomic DNA

Hi Folks,

I need to order some higher GC content genomic DNA. Any suggestions from where to buy?

I found out Streptomyces could be one possibility.

Thanks!
Forum: Sample Prep / Library Generation 12-11-2012, 10:24 PM
Replies: 20
Views: 27,357
Posted By Smriti
Hi Surfnturf, We have observed lot of...

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...
Forum: Sample Prep / Library Generation 12-10-2012, 04:02 PM
Replies: 1
Views: 2,391
Posted By Smriti
ds HS Qubit assay showing variability

Hi folks,

I am getting lot of variation in my genomic DNA concentrations when I measure it using HS assay. I always warm the DNA for 10 minutes at around 40C to improve its homogenity. Then I...
Forum: General 08-16-2012, 05:03 PM
Replies: 6
Views: 2,484
Posted By Smriti
Iadin: Both the links dont work. What should we...

Iadin: Both the links dont work. What should we do?
Forum: General 07-30-2012, 03:05 PM
Replies: 6
Views: 2,484
Posted By Smriti
Share "Building Novel Applications with Pipeline Pilot"

Hi there,

If you have downloaded this case study, could you please share with me. When I went to download it was already unavailable. That would be a great help. My email address is:...
Forum: General 06-20-2012, 11:59 PM
Replies: 14
Views: 3,248
Posted By Smriti
So, what are the conclusions from this thread: we...

So, what are the conclusions from this thread: we should store DNA aliquots in -20C and whatever present batch we are using in fridge. Also, to homogenize the DNA sample, we should either do gentle...
Forum: Sample Prep / Library Generation 06-18-2012, 12:07 AM
Replies: 16
Views: 9,829
Posted By Smriti
@Rocketknight, which assay of Qubit seems to give...

@Rocketknight, which assay of Qubit seems to give more accurate results, is BR assay consistent for your samples?
Forum: General 06-17-2012, 11:53 PM
Replies: 14
Views: 3,248
Posted By Smriti
Thanks! Dont you see slight shearing of this...

Thanks! Dont you see slight shearing of this genomic DNA by vigorously vortexing? And do you test your stock from time to time, to see if its sheared while kept in fridge, or for your applications,...
Forum: General 06-17-2012, 11:46 PM
Replies: 14
Views: 3,248
Posted By Smriti
Ok Thanks for this info! another quick question...

Ok Thanks for this info! another quick question that I have been asking others, how are you maintaining homogenity of your prepared stock? Dont you see variation in concentrations when you store it...
Forum: General 06-17-2012, 11:35 PM
Replies: 14
Views: 3,248
Posted By Smriti
@Heisman, which genomic (human) DNA have you...

@Heisman, which genomic (human) DNA have you used- male/female or generic? Have you done genomic library construction using it? Also, on website it says storage at 4C, did u store at 4C or -20C after...
Forum: General 06-16-2012, 10:59 PM
Replies: 14
Views: 3,248
Posted By Smriti
Thanks genericforms! I mostly aliquot stock...

Thanks genericforms!

I mostly aliquot stock genomic DNA after heating, diluting and freeze it. One by one I use the aliquots by transferring them in fridge for limited time. However, I observed...
Forum: General 06-15-2012, 04:21 PM
Replies: 14
Views: 3,248
Posted By Smriti
Thanks Heisman for quick response! Also...

Thanks Heisman for quick response!

Also while preparing dilution of genomic DNAs (Ecoli or human), how do you get homogeneous sample? Do you heat it around 37-45C everytime before using DNA for...
Forum: General 06-14-2012, 10:54 AM
Replies: 14
Views: 3,248
Posted By Smriti
Purchasing Human DNA (genomic)

Hi There,

Can anyone recommend me some vendor to buy Human DNA (intact genomic)? Once I bought Human DNA from Coriell Institute and that did not turn out to be a good quality DNA.

Quick...
Forum: Bioinformatics 06-11-2012, 05:30 PM
Replies: 1
Views: 1,151
Posted By Smriti
Alignment based sizing of inserts

Hi everyone,

I am new to the field of DNA sequencing. I need a quick help, can anyone explain me what do we mean by alignment based sizing of insert DNA and how different it is from physical size...
Forum: Sample Prep / Library Generation 05-25-2012, 02:09 PM
Replies: 2
Views: 2,915
Posted By Smriti
Thanks zsmith for your reply. So that means just...

Thanks zsmith for your reply. So that means just before shearing your sample, you heat every sample to 45C? And after shearing, just before analyzing also, do you heat it again?

Thanks again!
Forum: Sample Prep / Library Generation 02-16-2012, 10:07 PM
Replies: 2
Views: 2,915
Posted By Smriti
Genomic DNA sample preparation

Hi There,

I am new to handling genomic DNA so have certain experimental doubts:

1. When we prepare certain dilution of genomic DNA, how do we make sure that genomic DNA solution is homogenously...
Forum: Sample Prep / Library Generation 01-26-2012, 02:14 PM
Replies: 73
Views: 47,295
Posted By Smriti
Hi Hamid, I have been following all the...

Hi Hamid,

I have been following all the threads related to chromatin shearing on this forum. I kind of get similar result on IP showing larger fragments with high concentrations. Do you think...
Forum: Sample Prep / Library Generation 01-05-2012, 02:00 PM
Replies: 73
Views: 47,295
Posted By Smriti
Hi Hamid, In line to your explanation of...

Hi Hamid,

In line to your explanation of over-crosslinking of chromatin, I also did some preliminary work on chromatin shearing. I used Advance Analytical (Fragment Analyzer) and Agilent...
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