13 Questions 2 Answers 0 Followers
Questions related from Juli Elisa Udayani
I did sequencing run using PhiX control in Illumina's NextSeq 500 and found out the %PF only 0.4% yet the cluster density reached 267K/mm2. The reagent I used was fresh (not expired yet), it was...
22 August 2017 6,234 3 View
I stored my amplicons in -27 celcius and they are already purified to be used for Sanger Sequencing. However, my sequencing results were very poor, the sequence were almost not detected at all....
29 March 2016 4,119 5 View
I did COLD-PCR for JAK2 wildtype and mutant samples. The previous results were okay, the peaks were around 76-77 celcius. Now the peaks are around 77-78, I wonder what happened. My samples are...
04 March 2016 6,798 4 View
I am planning to use blocking primer for MEMO-PCR method so I will put a blocker in the 3' end. I wonder if C3 spacer and phosphate have differences in efficiency or others.
02 March 2016 6,425 0 View
I am going to detect BRAF v600e mutation in colorectal cancer sample and currently looking for appropriate methods to compare and to use. I am thinking of doing MEMO-PCR but still lack of...
08 February 2016 3,769 1 View
I use acrylamide gel with 8.5% concentration with 50ml volume but I think it takes too long waiting them forming unto gel, about more than 8 hours, even overnight. In contrast, my friend also use...
25 June 2015 1,827 4 View
I use Geneaid KIT to use the gel extraction protocol because I need to purify my samples that have been amplified with v1-v3 primer and reamplified with v1-v3 primer GC clamp. The results...
04 May 2015 3,278 2 View
I extract DNA from sweet potato and amplify it with v1-v3 16S primer then I re-amplify it again with GC-clamp to use it as samples for DGGE. The problem is, the result of GC-clamp primer PCR...
04 May 2015 9,120 6 View
My goal in my research is to analyse the dynamics of bacterial community structures in water samples from a zero-water discharge system. I might not sequence all the bands so I need to know if...
12 November 2014 1,743 1 View
I heard that rpoB is currently more trusted than 16S rRNA gene because rpoB gene is a single copy. Is it better overall to use rpoB than 16S rRNA gene since I won't sequence all of the band? The...
12 November 2014 4,185 6 View
As we know, there's limitation in DGGE that we can only use short number of basepairs. If we want to distinguish bacteria from some sample until the genus level with DGGE, what gene can we use...
11 November 2014 8,404 5 View
It's been common to use primer for variable regions in 16s DNA but I heard that it's not highly trusted anymore. I wonder what primer is now used for DGGE and where I can get it.
08 November 2014 5,380 4 View
I need to know the analysis method for the bands resulting from DGGE since every band is not highly trusted for showing one species--if every band is not sequenced. I wonder if there are any...
08 November 2014 627 4 View
