RNA Extraction

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Questions related to RNA Extraction

Is there any alternative to a fume hood when working with DTT?

I am going to work with dithiothreitol (DTT) whilst isolating DNA and RNA, so I was looking for a safe alternative to a fume hood, such as maybe a specific type of mask or anything different that...

18 February 2020 3,878 3 View

How to create "trait data" file for WGCNA?

As a biotechnology student in Shahid Beheshty University, Tehran Iran, I am very interested in systems biology area. Actually I need to know how should I create trait matrix file to reach Heatmap...

16 February 2020 1,834 3 View

TRIzol RNA extraction: No pellet after isopropanol precipitation even with glycogen?

So I'm using TRIzol for RNA extraction, but suddenly I'm getting no pellet during the isopropanol step *even though I added glycogen.* A few weeks ago I: 1. Took a large quantity of bacteria 2....

06 January 2020 8,512 5 View

Why is there no clear interphase during Trizol RNA extraction of fibroblast cells?

It looks almost as if the interphase is floating up into the aqueous phase during my extraction procedure. It doesn't form a distinct layer; it is very irregularly shaped and juts out into the...

02 January 2020 4,782 4 View

Reliability of Gel or Nanodrop ratios for RNA integrity and quality?

I have read somewhere that these should be only taken as a frame of reference? I am assuming that my samples with a 260/280 ratio of ~1.5 are too low, but when I run it on a 1% agarose gel, the...

26 December 2019 3,700 3 View

Why i am not getting the 2 layers/phases after adding 100% ethanol?

In isolation of DNA from trizol method, after adding the absolute ethanol in the phase left behind (RNA Extraction step) i am not getting the 2 layers to proceed further for DNA extraction and...

12 November 2019 1,473 2 View

Compatible of QIAseq Stranded Total RNA Lib Kit and Ribominus Transcriptome Isolation Kit?

Dear all, I'm going to perform RNA-Seq with a QIAseq Stranded Total RNA Lib Kit and depletion with Ribominus Transcriptome Isolation Kit/ Ribominus concentration Kit. Does anyone have...

29 October 2019 8,267 1 View

Low bacterial RNA yeld with RNeasy MiniKit?

Dear all, I am trying to do an RNA extraction of different bacterial species with RNAeasy mini kit, protokol #4 (lysozyme lysis + proteinase K digestion). Unfortunately, I have a fairly low...

28 October 2019 5,681 0 View

How can I improve the RNA extraction from cells?

Hello, I have problems with RNA extraction from cells. I work with primary neurons and astrocytes cultures, with 1*10^6 cells for each well (more or less, because some cells die). Actually, I use...

02 October 2019 1,661 5 View

How much cq value and error can be acceptable for reference and targeted gene in qPCR?

Dear Researchers, I did the qPCR, 20ul, (10 ul TB gree, primer 0.4, template 2ul, Water 7.2), steps, by using TAKARA, I got the following results, as you can see that with 1X, 3X, and 5X...

29 September 2019 4,370 9 View

What should do, if RNA quality is very low?

Dear Researcher I am working on passion fruit peel at ripening stages, and want to do qPCR but facing problem in getting good quality RNA from fruit peel, I have tried to extract the RNA...

28 September 2019 1,920 3 View

Which protocol for RNA Extraction from bacterial culture growing on aromatic compounds (problems with dark precipitations/polyphenolic compounds)?

During the course of the cultivation of a Pseudomonas sp. strain on a toluene derivative we observe a strong darkening of the media, supposedly because of polyphenolic (polycatecholic) compounds...

27 September 2019 9,897 6 View

RNA extraction from FAA fixed, methanol-preserved plant tissue. Is it possible?

Dear colleagues, I have a bucket of carrot's inflorescence buds that were fixed with FAA, dehydrated and stored in methanol at -20°C for ca. 3 months. I did ISH with some of them that worked fine...

23 September 2019 7,855 2 View

Can i use Tween-20 instead NP-40/Triton X-100 for separation of cytoplasmic and nuclear RNA?

Hi there. I want to extract separately cytoplasmic and nuclear RNA fraction from leukemic cell line by Trizol. Most of protocols that I saw suggests using a buffer with NP-40 or Triton X-100 for...

07 September 2019 2,489 3 View

What is the ideal timeline for differentiating Mono-Mac 1 cells with LPS?

We are currently planning experiments with the monocytic cell line Mono-Mac 1, which we will be using for HIV infections and analysis of different signaling pathways. As we are using them as a...

06 September 2019 3,452 2 View

What are the calculations to make a constant RNA concentration for different samples to do cDNA SYNTHESIS?

I have 2 concentrations from different samples, Nanodrop for each are 715.5 ng/ul and 467.5 ng/ul and approximately 2 ul was used for each sample. I am very confused on how to get and equal...

23 August 2019 3,635 3 View

How to extract RNA from cell cultured on hybrid scaffold composed of PCL and collagen?

Hi! We are doing studies about tissue engineering using hybrid scaffold composed of PCL and collagen. However get stuck in RNA extraction for gene expression analysis. Some study suggest using the...

19 July 2019 962 3 View

Why I lose my lettuce hairy roots RNA after extraction with licl method?

Why I lose my lettuce hairy roots RNA about 5 or 6 hours after extraction with licl method and on electrophoresis only it's DNA band will remain with no RNA? I do the extraction and I get the RNA...

10 July 2019 9,037 2 View

How to interpret our plaque assay results?

We have infected mosquitoes silenced for a specific protein with Zika virus . After a number of days we dissect the midgut, make a homogenate and try to check for virus replication by plaque...

11 June 2019 8,140 7 View

Hi guys i have extracted viral RNA and my nano drop reading 260/280 is 3.26 and 260/230 also 3.26 what may be the reason ?

I want to kno the reason why i got high value for 260/289 ratio and 260/230 ratio

07 June 2019 5,768 6 View

What is the best strategy to extract total RNA (Trizol) from crab gills?

Dear all I have tried 1ml Trizol to extract total RNA from crabs gills. The weight of most of my samples is + -0,03 g. We have applied this protocol for hepatopancreas samples and the results...

04 June 2019 1,545 8 View

RNA extraction from yeast showing only one band and no smears found. What could be the possible reasons?

I've been trying to extract rna from this particular yeast strain By611 and I could only get one band out of it. I am planning to run q-pcr after this step. Below I am attaching the picture of my...

05 April 2019 1,707 4 View

Where can I found information about coralline red algae physiology? Could Lithophyllum/Mesophyllum/Peyssonnelia physiology be related to substrates?

I'd like to understand better the physiological mechanisms involved in coralliceous encrusting algae grouth ( mainly Lithophyllum spp., Mesophyllum spp., Peyssonnelia spp.) in order to verify if...

07 March 2019 3,020 2 View

What is the best solution for obviating contamination with less RNA destruction?

we use trazol kit for extrcting RNA from sputum ;although we change our extraction kit we faced low 260/280 ratio of nanodrop.(1.5) according to well-known contamination of sputum...

30 January 2019 821 8 View

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