Asif Muhammad

11 Questions 10 Answers 0 Followers

Questions related from Asif Muhammad

Best tool to work out RNA secondary structure at various temperatures?

Can anyone please suggest some really useful tool to predict RNA secondary structure from a single RNA sequence but it should be capable of predicting structure of RNA at various temperatures....

25 August 2023 2,513 1 View

Is autoclaving adequate to eliminate/inactivate RNases in a solution?

I am going to try Oxford Nanopore sequence-specific direct RNA sequencing targeting one of my genes of interest. I have designed the primers and have them with me (Oligo A and Oligo B). In the...

12 July 2023 6,176 2 View

Why most of my long-read RNA sequences are aligned to mitochondrial genome?

I am using Oxford Nanopore RNA sequencing (Direct RNA minION) using total RNA from human cell line but majority of my reads are aligned to mitochondrial genome. Secondly, many reads for the genes...

01 June 2023 546 3 View

RNA long read sequencing using Oxford Nanopore minION affected by mild gDNA contaminated RNA sample?

I am intending to do minION RNA long-read sequencing using the Direct RNS sequencing protocol. I have successfully been able to quantify the RNA. However, some of the samples seem to have mild...

13 March 2023 4,729 2 View

What is the most reliable method for quantification of RNA; Qubit, Nanodrop or Bioanalyzer?

For the same sample these give different values so which one to trust?

21 February 2023 7,590 3 View

High throughput method for extraction of high quality of total RNA from human lung epithelial cells for Nanopore RNA sequencing?

I want to extract good amount of high quality RNA from human lung epithelial cells. I have pellets of nearly 1X10^7 cells per tube. I need very high purity total RNA that can be successfully used...

13 January 2023 1,829 1 View

What are MSTRG IDs in RNA-seq differentially expressed gene list?

I have my RNA-seq data analyzed and in my DEG file, there are quite a few MSTRG gene IDs with no gene name like MSTRG.115832.1 (Gene Name: #N/A). DO these correspond to any genes/transcripts or...

10 May 2020 8,044 3 View

How can I convert RNA-seq data (normalized read count and differentially expressed genes data in Excel format) in presentable graphical format?

I simply wanted to compare differentially expressed genes between 2 types of tissues using RNA-seq. Following, data was processed by a Bioinformatics person and provided 2 types of Excel...

03 May 2020 4,939 2 View

What is absolutely correct procedure for disposal of antibiotic solutions (vancomycin, gentamicin, kanamycin)?

Draining down the sink is always an easy option but not always the right way of disposal. Antibiotics like vancomycin are toxin and are not allowed at any level in animal products for human...

02 May 2017 1,952 3 View

What is the standard procedure for disposal of ethanol? Can it be drained down the sink?

Can individual labs formulate their own procedure for disposal of chemicals or is there a universally recognized system of procedures for disposal of chemicals?

23 February 2016 1,029 2 View

What is the composition of minimal media for growth of yeast?

I am looking for minimal set of components required for growth of yeast in general.

23 June 2013 9,972 1 View