Jawwad Ahmad

10 Questions 119 Answers 0 Followers

Questions related from Jawwad Ahmad

If I have to select between Gasteiger and AM1-BCC charge types, what is the best option here for my ligand?

If I have only two options in front of me to select either Gasteiger or the AM1-BCC, so based on which parameters or rules I can select the most appropriate charge scheme during minimization step...

19 July 2020 8,938 1 View

What impact would be there on RNA-SEQ experiments if we do not use any RNA Spike-In controls (like ERCC or SIRVs)?

Hi everyone, if I do not use spike-in RNA isoform controls for a customized RNA sequencing experiment (not the whole transcriptome, just based on few specific genes we are interesting), so is...

09 February 2020 7,306 2 View

What is the minimum and maximum cDNA input from FFPE samples in library preparation phase to perform the RNA SEQ by Ion Proton?

Dear All, 1 ug of permissible quality FFPE RNA is transcribed to cDNA through SSIV VILO RT kit. I have Qubit v.4 device, which can measure cDNA to a good extent. The cDNA ranges from 25-100 ng /...

12 November 2019 2,139 1 View

Is there any undesirable effect of bacterial RNA load of normal intestinal flora present on human colon samples for the gene expression analyses?

It is a known fact now that interactions between bacterial (normal flora) and colon cancer cells influence the transcription profile of host cells or enterocytes. So, how can I avoid or minimize...

12 October 2018 9,587 1 View

For customized mRNA sequencing, can I omit the rRNA removal procedure step, which is offered by several commercial kits?

If I am interested in a customized mRNA-only Sequencing (RNA-Seq) based on few transcripts (not the whole transcriptome), and after having satisfied & permissible RIN values for my extracted...

22 September 2018 1,904 3 View

Does "No Primer Dimer Formation" guarantee the absolute utilization of entire primer content (F & R both) in a PCR reaction?

Dear all, in a PCR (conventional & realtime both), if we achieve our desired product (GOI) and along with, there is also no primer dimer (PD) formation seen on the gel and melt curve, does...

03 November 2017 10,040 3 View

Why does the HRMA (High Resolution Melt Analysis) cannot detect homozygous variants properly than heterozygous ones?

Any explanative thoughts or information? Will the 2nd or 3rd melt of products attribute to some improvement for their detection?

21 October 2017 8,670 3 View

How an Asymmetric qPCR (unequal forward and reverse primers) results in an improved Melt Curve?

A low concentration of a primer than the other one in high concentration or even in volume often exhibits good melt curve appearances. What could be the reasons behind this? Is this dependent on...

28 November 2016 7,782 3 View

For Crime-Scene Genetics, apart from AMELY & AMELX, are there any other genetic markers used for the sex determination of an unknown?

So if any gene which is not in a single copy form, can we use it?

21 November 2016 6,606 3 View

What strategies we can adopt to avoid Retropseudo genes to get amplified during a Sybr Green based qPCR run?

And how to recognize such amplifications on the basis of Tm in the melt curve stage? As it is a known fact that retropseudo genes have no introns and they can be amplified at cDNA level along...

07 November 2016 7,636 2 View