Why doesn't cell-free DNA immediately degrade in the circulation?

More Marc Paul O'Sullivan's questions See All

What additional information do I need for a gene expression a priori sample size calculation?

We want to calculate the sample size for a future study: We have two groups called cases and controls We want to set alpha value at 0.05 We want to set power at 0.8 We want a fold change of...

06 July 2019 1,600 5 View

Can you perform a second log transformation on 2^-DDCT to further reduce the skew?

Can you perform a log transformation, i.e. Log2 on your 2^-DDCT data to reduce the skew, thereby performing parametric tests as these may be more robust and reliable than non-parametric tests.

02 March 2019 7,136 3 View

Citations on log transformation of DDCT-PCR results?

I was recently told at a PCR based workshop that DDCT-PCR data should always be log transformed to the ^2 or ^10 as it allows a normal distribution for your results and allows you to use more...

31 December 2018 5,667 3 View

How to best use miRNA target/pathway prediction software and resources?

I'm sure many people know there are a large number of prediction softwares' available online, with most including high throughput and low throughput validation. Most of these have a filter list,...

05 June 2018 5,907 0 View

MiRNA Upregulated in NGS and Downregulated in RT-qPCR?

We've recently ran an NGS, had it analysed and tried to validate using RT-qPCR? Two of the miRs were significantly changed in both NGS and RT-qPCR but in different directions, i.e. one was...

09 October 2017 1,283 9 View

Regarding how much cDNA is made in a cdna reaction?

If you start off with 20ul of 20ng/ul of total RNA, and you need 4ul of this for a 20ul cDNA reaction (4ul template RNA + 16ul of enzyme and buffer mix). My understanding is I've input 4ul of...

02 March 2017 9,491 3 View

What yields better results microarray or next generation sequencing?

Specifically for miRNA, but also interested in RNA in general

10 November 2016 9,831 7 View

Good reviews on comparisons between serum and plasma?

I'm quite eager to find papers that compare the make up between serum and plasma, that goes beyond the fact that plasma is treated with an anticoagulant, unlike serum which is allowed time to...

10 November 2016 4,643 0 View

What are the main pathways involved in oligodendrocyte development?

Are there any seminal papers on pathways in oligodendrocyte development?

04 May 2016 9,198 2 View

Would miRNAs in whole blood still be considered circulating miRNA, or would this be primarily in serum and plasma?

In some questions asked by others, I see people categorizing circulating miRNA as only miRNA from serum and plasma, shouldn't miRNA from whole blood also be considered circulating miRNA?

04 May 2016 8,601 5 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

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 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

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

LEDs on Vis Light photo degradation of MB water sol via N doped TiO2 in a mini flume?

Good day to all, I have no experience with light emitting diodes. I am building a glass mini flume to demonstrate the photo degradation of Methylene Blue in water running over self cleaning...

26 February 2021 4,026 5 View

Why do a weight decrease for thermal degradation in nitrogen gas condition?

Hi all The question is related to TGA(Thermogravimetric analysis). Thermal degradation easily understood but why do samples weight decrease? altough just binding is broked, the weight of...

26 February 2021 1,100 5 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

Steps to calculate activation energy by coats & redfern method?

I'm a chemistry student and I'm researching the kinetic degradation of mixed plastic waste. I'm having trouble calculating the activation energy by the coats & Redfern method. The data that...

24 February 2021 974 1 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

Craig Silver

It is degraded. cfDNA is typically very fragmented and shorter than genomic DNA. The reason why it isn't MORE degraded is that blood isn't that intolerable for nucleic acids.

Marc Paul O'Sullivan

Craig Silver thank you for your response. To ask you a final follow on question, is it protein bound/within extracellular vesicles or is it completely free?

Both forms exist. Exosomes are lipid/membrane encased nucleic acids, as well as free circulating DNA that is shed by cells.

Nirali Shukla

So for how long can one store plasma,serum and CSF as biological specimens at -80C for cfDNA extraction?