It really depends on what the sample is. For many applications Qiagen kits are fantastic, for others not. For example, I used a CTAB extraction method for the green alga Chlamydomonas and used it for genome sequencing with Illumina and the results were very good. In contrast, commercial kits didn't work well. Generally, I would recommend using a protocol optimized for your sample type as the result can vary a lot.

I prefer to use a column based kit (i.e: Qiagen's), they're good for consistent 260/280s and 260/230s, high throughput, and working with small amounts of precious sample.

I suppose it depends on what you are extracting from, but we use Qiagen kits and they have proven to be reliable and consistent.

It depends on the type of DNA and the material from which you are extracting it. For extracting bacterial DNA from feces, I use the Qiagen genomic tips. I get a higher yield with this method. You should combine the tips with a bead-beating step or freeze/thaw step to break down the bacterial cell walls.

If you are extracting bacterial DNA from soil, then I would suggest using the MoBio powersoil kits.

I am a fan of ph/ch method!... However, it depends on several factors. If you have very small amount of tissue, go for phenol/chloroform. I have had very good yield even from FNAs with small amount of tissue. If you have more tissue -and more money! but less time- go for column. The major issue with ph/ch is the contamination of the final yield which can be avoided by being patient and pipetting accurately. The major issue with column is that some of DNA may trap in the column. There are simple methods to avoid having chemicals in the final isolated DNA by ph/ch method.

Hi Philip,

Melissa is right, the method will depend on what is your initial sample. We at MO BIO Laboratories have Kits for different scenarios. We offer FREE samples so you can try the kits for free. We also have an amazing technical support team that can guide you to the best option based on your project. www.mobio.com

I hope this helps!

Hi Philip,

I pressume that you are looking for a protocol to extract DNA from bacteria. Here is the protocol to extract high quality and quantity DNA protocol, This worked perfect for Gram possitive bacteria and I have got plenty of DNA with good quality which was used for whole genome sequencing.

Chromosomal DNA was isolated from the overnight cultures as follows. Briefly, stock cultures were streaked onto MRS agar and a single colony was used to inoculate into 15 ml MRS broth. Following overnight incubation, cells were collected by centrifugation at 5000 g for 10 min. The cell pellet was resuspended in 5 ml of PFGE extraction buffer (75 mM NaCl, 25 mM EDTA, 20 mM Tris, pH 7.5) containing 30 mg/ml lysozyme (40,000 U/mg) (Sigma-Aldrich, Ireland) and 10 µl of mutanolysin (750 U/mg) (Sigma-Aldrich, Ireland). The cell suspension was incubated overnight at 37oC with gentle mixing (~5 rpm) using a roller mixer. Subsequently addition of 1.5 ml of 10% [w/v] sodium dodecyl sulphate (SDS) and 10 mg/ml proteinase K (7.5 U/mg) and incubated overnight at 55oC with gentle mixing (~5 rpm). To the cell suspension 2 ml of 5M NaCl and equal volumes of Phenol:Chloroform:Isoamylalcohol (PCIA) (25:24:1) (Sigma Aldrich, Ireland) mixture was added and incubated for 30 min at room temperature with frequent inversion. The mixture was centrifuged at 5000 g for 10 min and the upper phase was collected into a new tube, to which an equal volume of PCIA was added. The suspension was mixed gently and centrifuged at 5000 g for 10 min (repeated 2 times). Finally, to the collected upper phase, 1.6 ml of 3M sodium acetate and equal volumes of absolute ethanol (-20oC) were added and mixed gently prior to centrifugation at 5000 g for 10 min. The supernatant was discarded, and the pellet was washed with 70% [v/v] ethanol. The residual ethanol was removed and the pellet was dried at 37oC. Finally, the pellet was resuspended in 2 ml of TE buffer contain 0.1 mg/ml RNase (81 U/mg) and stored at -20oC.

If you have any queries regarding this protocol or any optimisation required you can reach me on : [email protected]

Good luck

Cheers

Aditya

We use the column-based GenElute kits from Sigma-Aldrich to obtain chromosomal DNA from bacteria for Deep Sequencing and the DNA quality is very good and the sequence reads have been excellent. I have done phenol/chloroform for years but would not go to it back unless there are very specific circumstances.

Good luck,

Christian

Puregene kit. The best. Leave dna to digest overnight.

Check our protocol in formaline fixed paraffin embedded tissue springer

What method of DNA isolation to use depend greately on what kind of material you'll use and main goal of your investigation. Also it will depend on what genome study you want to run and based on what method (Sanger, Illumina (NGS), 3-rd generation sequencing or other).

I used to work with Qiagen-Spin column kits for direct sequencing, microarray Chips, or NGS. The ready-spin Column protocol is recommended by the above-mentioned strategies.

Depending on the initial sample (material), total genomic DNA can be extracted using different methods. However, if you want to extract bacterial DNA from soil, I'll recommend Power Soil DNA Extraction Kit (MOBIO) for good results.

if it is bacterial DNA means you can follow the protocol from Sambrook manual.

We use the GenElute kit to extract from small amounts blood. It gives DNA pure enough for any application, including NGS. For DNA from saliva, we use the Oragene collection kit, that includes reagents for a very easy extraction protocol. DNA quantity and quality are exceptional, although the product is pricey.

Hi, I am used extracted the DNA by DNA extraction kit spin-column (Qiagen) or (BIOTEKE) from long period, the yield DNA was subsequently entered in PCR and sequencing with good results, try these kits and you will get much better results

Check the following link

http://dx.doi.org/10.1016/j.vetpar.2013.08.003

Qiagen provides many extraction kits suitable for any starting material I believe. It depends on spin column. For my blood samples, I used it for PCR, LR-PCR, microarray and NGS,

I used DNA extracted from Qiagen's extraction kit. Quality and quantity of DNA obtain using kit very good for for various various uses like sequencing.

We used Qiagen-Spin column kits to isolate DNA from blood. The quality was excellent. We performed all our GWAS analysis on these samples

DNA extracted by phenol chloroform method can be used for genomic applications like next generation sequencing as far as my knowledge is concerned.

we have successfully used the Qiagen maxi and mini DNA extraction kits. Purity was very good, DNA integrity as well, RNA was fully digested. I would go for the Qiagen kit again.

It really depends on what the sample is. For many applications Qiagen kits are fantastic, for others not. For example, I used a CTAB extraction method for the green alga Chlamydomonas and used it for genome sequencing with Illumina and the results were very good. In contrast, commercial kits didn't work well. Generally, I would recommend using a protocol optimized for your sample type as the result can vary a lot.

My experience says that the organic method of DNA extraction is the best method for best quality DNA for genomic applications. Researcher need to do it properly and must use molecular biology grade fresh chemicals,

I use QIAGEN kit for DNA extraction and it works fantastic for DNA microarray.

I also use Qiagen kit for DNA to be used DNA forensic analysis. It works well but I never used thier Maxi kits. I am sure it will also produce good quality DNA.

It depends upon the kind of sample you have. We use UltraClean® Soil DNA Isolation Kit from MoBio to get DNA from soil samples. But if the sample is from a polluted soil, we need to do a downstream phenol:chloroform extraction to obtain DNA clean enough to apply NGS technologies

I always use Qiagen-spin columns and the results are excellent.

I would like to think there is no best DNA preparation method unless the sample type is known. Plants require more complex protocols than animals or microbes. Asuming you need to prepare DNA from mammals, I would advise against using Phenol/Chloroform, as you will loose a lot of material by the salt-ehtanol precipitation step and recovery.

Important in selecting a suitable method is the inclusion of a proteinase K digestion step, which is followed by an affinity step using silica or similar principles. These methods are fast, reproducible, yield to clean DNA (A260/A280 > 2) and the fragment sizes will be about 40 000 kb.

I hope this herlps

Good luck

I think many have suggested this in their answers, but I'll just point it out directly. As posed, your question can't be answered. Let me offer an analogy. I'm a photographer when I'm not in the lab. People often ask me "what is the best photography bag". I usually laugh. I own no less than 5 bags. There is "the big one" that holds everything I own, but is too big and heavy for hiking. There is the traveler, which can be used for international carry-on baggage. The "padded one", which is bulky but protects the equipment like no other. In short, there is no "best bag" unless you qualify with "best bag for..." Back to genomics. It depends on two very important factors: your starting material and your final application. Our group is finishing up a project that evaluated DNA extraction protocols from different starting materials. Starting materials included Formalin fixed tissues, plant materials, ethanol preserved tissues, water samples, dried tissues... The final application was next generation sequencing. In short, depending on the starting material, there were at least 3 "best methods". "Standard column-based" kit work well with the easy stuff (ethanol preserved soft tissues), but in house protocols were always best with more difficult materials. In short, I would say ask a specific question, and then you'll get a useful answer.

Cheers,

Mark

To my knowledge, you can get away with anything if you work on vertebrates. I usually work on marine invertebrates (crustaceans, mollusks and tunicates) and have yet to identify a method that works well. It may be because the tissues of these animals contain inhibitors that are not present in the vertebrates.

Salting-out and Qiagen kit definitely produce poor results, and DNA that is run on a gel tends to be a bit smeary. CTAB is also not great. I've had more respectable results with the EZNA Mollusc DNA extraction kit, but the results are really a mixed bag and I'm not sure why.

If anyone can suggest an approach that works well for marine invertebrates, I'd like to hear about it.

Cheers,

Peter

We use modified protocol from Qiagen kits to extract DNA from semen, and use DNA for Illumina microarrays.. I think? its the best method for thus type of sample..

We used spin coloumn methods from different companies to isolate mammalian and plant DNA for NGS and they were all fine, but even the same product works differently in different hands, as you can see from the above discussion. For amplicon seq I isolated fragment from gel using Zymo's kit and that produced very nice reads.

spin-column DNA extraction kits Roche, Qiagen or Bioteke have high quality and yielded high amount of pure DNA and I used them from 5 years ago

I would agree with everyone who said there is no best extraction method. Quite often, it depends on the application and the user. We use Qiagen to isolate human genomic DNA from buccal swab and follow this up with ethanol precipitation. The result is a good yield of very clean DNA. But others have had similar success with other commercial kits. You may consider trying different commercial kits to see which works best in your lab.

I generally do not recommend phenol/chloroform. Even after precipitating with isopropyl we have seen samples submitted with phenol still in them. This has been problematic particularly in automated sequencing.

Hi Philip,

I agree with the answers above. It depends on where are you extracting the DNA from. MO BIO Laboratories have kits and protocols for DNA extraction from different samples types. MO BIO offers free sample kits to you can try the product and decide which one works better for your experiment. http://www.mobio.com/samples

 Hi Peter in response to your earlier question, on marine DNA extraction, may I suggest this kit: EasyPure Marine Animal Genomic DNA Kit

http://www.aasinc.co/shop.html#!/EasyPure-Marine-Animal-Genomic-DNA-Kit/p/52930604/category=139123

Thanks Onikepe, it's definitely worth a try.

I have the same question to ask. I would like to isolate genomic DNA from gram negative bacteria for sequencing to determine the presence of a specific gene. May I know what isolation method should I use for that purpose? Thank you. 

Hello! I was interested in the same question - Does any of you can advise me regarding a specific kit for tissue extraction of  DNA  ? thanks in advance

Hai every one i have to ask same question but hear we isolate DNA from cervical cancer tissue (collected in RNA later) I was using the phenol/chloroform method, but DNA isolated using this method may contain residual phenol and/or chloroform, which can intrept  in downstream applications  e.g. DNA micro array, whole genome sequencing and NGS. 

Is there any manual method to isolate DNA from tissue

lack funding’s we are not go to KIt based methods

one of my friend suggest use  guanidine hydrochloride buffer (10 mM Tris HCl, pH 8.0, 0.1 M EDTA, pH 8.0, 6 M guanidine hydrochloride and 0.1 M sodium acetate)

what is the best method to isolate DNA from tissue?

I am wondering you are going to use your isolated DNA templates in NGS or micro-array methods, but you could not have a budget for DNA isolation kit. 

I want to extract genomic DNA from whole blood.Can any one suggest shortest manual method.Phenol-chloroform method is quite time taking.

Do you think is there any problem if I used ATMAB instead of CTAB for NGS? Or if I used diclhloromethane instead of chloroform? I work with trees and sometimes the DNA extraction is very difficult. Thanks!

CTAB may yield good DNA, but not very clean. Best extractions (clean, abundant, pure DNA) are normally achieved with extraction kits such as Qiagen.

Hello everyone..I have the same question about genomic DNA extraction.

We are planning to do whole genome sequencing by using Ion S5 XL System (Ion Torrent).

I would like to know which is the suitable extraction kit to be used.

Our samples are gram positive and gram negative bacteria.

can anyone recommend a reliable method for good quality genomic DNA from Drosophila? I would need to do NGS with the genomic DNA extracted.

It depends on what the sample .