How to build miRNA sequence from the RNA-seq data assembly from NCBI with Geneious Prime software?

Ahmad Fadil Rizkyantoro @Ahmad-Fadil-Rizkyantoro

03 July 2023 1 445 Report

I need a guidance from my research fellows in Bioinformatics here who are knowing on how to make miRNA sequences from RNA-seq data from NCBI with software such as Geneious Prime for instance as I am a beginner at this (RNA-seq assembly for miRNA). Thank you.

Frederic Lepretre

Hi Ahmad

before going to the software, be sure the samples were extracted with the right protocol and kits to allow miRNA to be selected or selected in the whole samples.

fred

Badges
Science method

More Ahmad Fadil Rizkyantoro's questions See All

Is IMPACT FACTOR justified in case of Taxonomy?

There is huge pressure of getting good impact factor on scholars now a days. On the other hand Taxonomy is a very dry subject and the concerned papers can only get citation in same group of organism.

26 February 2021 5,851 1 View

Why tick's salivary gland extract didn't run in the gel (SDS PAGE )??

Greetings, I want to make SDS PAGE for my sample (Tick salivery gland extract), I tried concentrations 10%, 12%. I also tried high molecular weight ladder. But the protein stopped at the top and...

25 February 2021 7,698 3 View

Is it possible to set a breakpoint at a specific DYNAMIC instruction using the GNU Debugger (GDB)?

Using GDB, it is straightforward to debug and monitor a target program by setting a break-point at a specific instruction, since the instruction addresses are known. However, we have two...

24 February 2021 1,598 2 View

How to measure the pH of Peat Soil?

Peat possess organic content above 75% and is highly acidic in nature (i.e. pH < 4). Before commencing stabilization, it is mandatory to know about the pH level of peat. Therefore, your...

18 February 2021 9,424 7 View

How to Measure Consumer Willingness To Change from petroleum-fueled vehicle to electric vehicle?

I wanted to calculate the probability of one consumer shifting from using a petroleum-fueled vehicle to an electric vehicle. Since my background is in engineering I do not know much about how to...

15 February 2021 9,190 5 View

Having trouble mounting the sections on the slides for IHC staining, what solution should I use?

Hello everyone, I just started learning IHC staining and I have some frozen sections to practice with in a 96-well plate. I'm having trouble mounting the sections on the slide, a colleague told me...

08 February 2021 6,880 3 View

How to use Image Lab to take an image for the bands and the ladder in the same image merged together in Western Blot?

Hello everyone. I was trying to use Image Lab software to take an image of both the ladder and the samples merged together in one image to see the position of the bands according to the ladder MW,...

04 February 2021 9,996 2 View

Need a research paper for multi speaker and single microphone acoustic echo cancellation?

Hi, I am working on a problem that involves multiple smartphones/tablets. All devices are playing the same sound with synchronization difference up to +- 5ms. Now, there is an echo issue and I...

02 February 2021 5,929 3 View

Can I use the result from a pilot study to decide the minimum sample size ?

Can I use the result from a pilot study to decide the minimum sample size required to compare the means using independent sample t-test ? Or any other way that can help me to determine the...

29 January 2021 7,677 6 View

How to prepare secondary antibody from lyophilized antibody?

So I'm new to lab research and learning Western Blots these days. I ordered my secondary antibody and it arrived in a powdered form. Here is the...

27 January 2021 5,402 3 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

Can MicroRNA cross the blood brain barrier?

In diseased conditions, many genes and gene products are visible in the bloodstream. So my question is whether we can find traces of microRNA which is involved in disease and disorder in blood serum?

24 February 2021 7,064 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View