Sunday, 7 February 2016

Our first paper on the bioRxiv

I just uploaded our paper, which has also been submitted to BioTechniques, onto the bioRxiv preprint server. The work we present comes from an idea I had shortly after first using Agilent's BioAnalyser in 2000. I was blown away by this piece of technology that has become the de facto standard for RNA QC, and has also pretty much replaced gel electrophoresis for DNA fragment analysis in NGS applications. When launched in 1999, it was the only microfulidics instrument for biology applications. The idea was a simple one: can bioanalyser chips be swapped between assays?


Figure 1: qualitative analysis of the same sample across different chips


In Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA we show that for RNA and NGS library size they most certainly can. We evaluated the compatibility of two of the most commonly used BioAnalyser kits (RNA6000 and DNA-HS) with three BioAnalyser chip types (RNA6000, DNA1000 and DNA-HS). Importantly, the sticker displaying the chip layout was disregarded and the loading pattern indicated in the assay-specific protocol was used in each experiment. Concentration and RIN of each RNA sample were highly comparable within and between chips, and well within the normal variability expected of samples submitted for RNA-seq experiments. For NGS libraries the average size estimated across all Bioanalyzer chips was 290bp with a 40bp range across all samples, while DNA concentration showed a 10-20% variation in concentration across chips.
Although the quantitative analysis of DNA (NGS libraries) was not so great  we'd always recommend quantitative PCR. Our quantitative results appear to be due to higher variability for concentration data between chip types, although this was due to inter-chip variability and not due to chip type. I've never been a fan of using the BioAnalyser for quantitative analysis, except perhaps in RNA-seq or microarrays where the amount of RNA being used is often less critical. 
Jess and Tom did the work in the lab and drafted the manuscript. This paper has been long in the making. Although the idea is nearly twenty years old it was "sat on the back boiler" for a long time while other more important work got done. In the end it was only a few days of lab work and we spent more time in the writing and correspondence than Jess or Tom spent in the lab. BioTechniques may only have an impact factor of 3 compared to Nature Methods 30, but it is a well respected journal that publishes lots of very useful articles. It is one of the journals I have read the longest and still puts out lots of great work.

bioRxiv: I've never put a paper up on the bioRxiv before but am a fan of the philosophy (although it is not the perfect publication platform). The University of Cambridge encourages work to be published in open-access format and I hope this will help get the work into the hands of people who want to read it. Our posting on bioRxiv is an extra push to make our data, and conclusions, freely available. We also get a DOI so the work can immediately be cited.
The paper has been published under the most open "CC-BY" license so anyone can share, reuse, remix, or adapt this material for any purpose, providing the original authors are credited and cited. option as the most liberal in terms of re-use, data mining etc.

I'm now waiting for the article screening process on bioRxiv to be completed so I can update the post with the DOI.

20 comments:

  1. It is all about how we interact with the problem. The qualitative article critique give us wide range of research on the same topic.

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    Replies
    1. Happiness is all i see now I never thought that I will live on earth before the year runs out. I have been suffering from HSV 1&2 for the past 3 years now; I have spent a lot of money going from one places to another, , hospitals have been my home every day residence. Constant checks up have been my hobby not until this faithful day, I was searching through the internet, I saw a testimony on how Dr sigolo helped someone to cure HSV 2, quickly I copied his email which is DR.SIGOLOHEALERTEMPLE@GMAIL.COM just to give him a test I spoke to him, he asked me to do some certain things which I did, he told me that he is going to provide the herbal cure to me, which he did, then after using the herbal medication for 2 weeks, he asked me to go for medical check up which i did and I was free from the HSV1&2, he only asked me to post the testimony through the whole world, faithfully am doing it now, please brothers and sisters, he is great, I owe him in return. if you are having a similar problem just email him on DR.SIGOLOHEALERTEMPLE@GMAIL.COM You are the next person to get cured.
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    3. Hi Friends i am so glad to writing this article today to tell the world how Dr Unuareghe cured my HSV VIRUS,i have been detected with HSV-1 AND HSV-2 since five years ago, ever since then my life has been in complete bizarre and agony,i have used so many drugs that was prescribed to me by several doctors,but it didn’t cure my HSV VIRUS neither did it reduce the pain,until a certain i was checking for solution in the internet,then miraculously came across Dr Unuareghe the powerful herbalist that cure numerous individuals HSV-1 AND HSV-2 INFECTION,then i contacted his email: dr.unuareghecuringhome@gmail.com i explained everything to him and prepared a cure that cure my HSV-1 AND HSV-2 disease totally after receiving his herbal medicine, so my friends viewers why wait and be suffer when there is someone like Dr Unuareghe that can cure any disease HIV/ CANCER/ HEPATITIS B VIRUS, you can contact his via:dr.unuareghecuringhome@gmail.com or watsapp +2349067894643

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  2. This was an amazingly helpful tip as we always seem to have excess RNA chips to use up! I tested this for RNA pico chips and these can also run as a DNA chip following the instructions in this paper. Thanks James!

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  3. My name is Antonio Jefferson Cole, I'm in Salt Lake City, Utah. It is a pleasure for me to write this testimony about how I got healed from genital herpes 12 hours ago. I have read so many comments from some people who have been cured of HIV by Dr. Ekpiku, but I never believed them. I was hurt and depressed, so I was very curious and wanted to try Dr. Ekpiku, so I contacted him on his email Ekpikuspellhomeofgrace@gmail.com when I get in touch with him, he assured me 100% that it will heal me, I begged Him to help me. My treatment was a great success, he healed me as he promised. He sent me his medication and asked me to go for check-up after 2 weeks of taking the medication. I agree with him, I took this medication and went to the check-up after 2 month, to my greatest surprise my result was negative after treatment, I am really happy that I am healed and healthy again. I waited for four months to make sure I was completely healed before writing this testimony. I did another blood test today and was still negative Herpes, so I think its time I tell someone out there with Herpes HSV-1 or HSV-2, HIV, HPV, hepatitis B, diabetes, cancer and so on, Dr. Ekpiku in the email: Ekpikuspellhomeofgrace@hotmail.com . Your phone number is +2348073673757, He is also on whats app. I completely understand how you can feel skeptical about it, because it happened to me, it can be expensive for you, but I'm telling you now that there is a cure for these diseases and I am a living witness firsthand.or you can email me on antoniojeffersoncole@gmail.com for any assistance.

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  5. I want to thank the God of DR boadi, who will believe that a herb can cure 10
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    she told me that he is well known in curing HIV/AIDS, HERPES (HSV1, HSV2) and CANCER etc.
    I decided to email him, unknowingly to me that this will be the end of the HIV aids in my body, he

    prepare for me Herbs, and gave me instruction on how to take it, at the end of
    two weeks, he told me to go to the hospital for a check up, and i went,
    surprisingly after the test the doctor confirm me negative, i thought it
    was a joke, i went to another hospital, it was also negative, then i introduce
    my friend who was affected with Herpes disease to the Dr, after taking the Herbs the DR. send to her,
    less than two days the inching stop, less than 2 weeks she was completely free and healthy again.
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  6. I used to suffer from HERPES SIMPLEX VIRUS for about 3 years. No medications or treatments ever really did anything for me (i tried them all no one work. but I was actually able to completely cure HERPES naturally after countless hours of online research. What worked for me is as follows: I saw Dr ILLUOBE Information online that he normally cure and treat disease and infirmities with his Herbal Medicine, I never really believed the people who where recommending him thou i saw on blog about 6 people where also testifying on how they were cured by Dr ILLUOBE, and still Ellen recommend Dr ILLUOBE who uses herbal medication to cure HERPES SIMPLEX VIRUS and gave me his email, so i mail him He told me all the things I need to do and also give me instructions to take, which I followed properly.Before I knew what is happening after two weeks the HERPES SIMPLEX VIRUS that was in my body got vanished. so if you are also heart broken and also need a help, you can also email him: drilluobehealinghome@gmail.com. if you are infected with any disease like HIV,AIDS, CANCER,HERPES SIMPLEX VIRUS, or any other disease you can also be happy like me by contacting.....
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  7. Hello viewers! i am so glad to writing this article today to tell the world how Dr Ogala, cured my HIV VIRUS, i have been detected with HIV virus 2 years ago, ever since then my life has been in complete bizarre and agony, i have used so many drugs that was prescribed to me by several doctors, but it didn't cure my HIV VIRUS neither did it reduce the pain, until a certain i was checking for solution in the internet, then miraculously came across Dr. OGALA the powerful herbalist that cure numerous individuals HIV INFECTION, then i contacted his Email: ( ogalasolutiontemple@gmail.com ) i explained everything to him and prepared herbal medicine that cure my HIV disease totally after receiving his herbal medicine. So viewers why wait and be suffer when there is someone like Dr OGALA, that can cure any disease HIV/ CANCER/ HEPATITIS B VIRUS, you can contact his via E-Mail: ( ogalasolutiontemple@gmail.com ) Or call his number (+2348110496023)

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  8. IT IS REAL!!! HOW I COMPLETELY GOT RID OF 4 YEARS GENITAL HERPES WITHIN 7 DAYS... GOD IS AWESOME!!!!....

    I have been dating for almost 7 years until i contracted GENITAL HERPES VIRUS from my Ex-boyfriend. Ever since then i have been searching for cure everywhere because i was feeling so uncomfortable having so many outbreaks, Most people have herpes in one form or another, i was first taking Antiviral medicines such as acyclovir (Zovirax), famciclovir (Famvir), and valacyclovir (Valtrex), which are recommended for treating primary genital herpes outbreaks..But i needed to get rid of it completely, I came across so many testimonies online speaking about cure to herpes. i was so eager to be completely cured, I became a victim of fraud after contacting several so-called herbal doctors i was referred to. I lost a lot of money but i didn't stop searching for a cure.
    Then one faithful day,i came across a testimony of a lady saying that she got her Genital herpes cured by a GREAT HERBAL DOCTOR she called Dr. Aramide by contacting him through his email address and including his telephone number.And she advised anyone with GENITAL HERPES or SIMPLEX HERPES to contact the herbal doctor for HERBAL CURE. I contemplated for about 4 hours whether or not to contact him. Then something inside of me told me to give a try. I then contacted him through his email and told my problems to him. He told me all the things I needed to do and also gave me instructions to follow, Which i did properly.Just within the 7 days of drinking and applying the herbal medication he sent to me through DHL delivery service, I started seeing changes i went to a medical doctor for check-up, I was so happy when the doctor told me i was no more having GENITAL HERPES VIRUS,it was all tears of Joy from that moment, I never thought HERBS could cure HERPES and if i could ever meet a GENUINELY GREAT HERBAL DOCTOR. I'm so grateful to him. i am completely free from GENITAL HERPES VIRUS,i recommended him to a family friend having Simplex Herpes virus, He called me and told me he is also cure completely. I promised to share my own testimony like that of the lady on the internet. If you are also having
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    ReplyDelete
  9. Hi Friends i am so glad to writing this article today to tell the world how Dr BAWADA cured my HSV VIRUS,i have been detected with HSV-1 AND HSV-2 since five years ago, ever since then my life has been in complete bizarre and agony,i have used so many drugs that was prescribed to me by several doctors,but it didn't cure [my HSV VIRUS neither did it reduce the pain,until a certain i was checking for solution in the internet,then miraculously came across Dr BAWADA the powerful herbalist that cure numerous individuals HSV-1 AND HSV-2 INFECTION,then i contacted his email:drbawadasolutionhome@gmail.com i explained everything to him and prepared a cure that cure my HSV-1 AND HSV-2 disease totally after receiving his herbal medicine, so my friends viewers why wait and be suffer when there is someone like Dr BAWADA that can cure any disease HIV/ CANCER/ HEPATITIS B VIRUS, you can contact his via:drbawadasolutionhome@gmail.com or his Mobile number:+254741086480 OR web/site
    http://drbawadasolutionho.wixsite.com/drbawada

    ReplyDelete
  10. I am so Happy to be writing this article in here, i am here to explore blogs forum about the wonderful and most safe cure for HERPES SIMPLEX VIRUS . I was positive to the deadly Virus called HERPES and i lost hope because i was rejected even by my closet friends. i searched online to know and inquire about cure for HERPES and i saw Dr OMOYE testimony online on how he was cured so many persons from Herpes Disease so i decided to contact the great herbalist because i know that nature has the power to heal everything. i contacted him to know how he can help me and he told me never to worry that he will help me with the natural herbs from God! after 2 days of contacting him, he told me that the cure has been ready and he sent it to me via DHL and it got to me after 14 days! i used the medicine as he instructed me (MORNING and EVENING) and i was cured! its really like a dream but i'm so happy! that’s the reason i decided to also add more comment of Him so that more can be saved just like me! and if you need his help,contact his Email now (dromoyespellcastertemple@gmail.com) or him on whatsApp number:+2349034412845 ..

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  11. Dr Benson, God will continue to bless you more abundantly, for the good works you have done in so many peoples life's, including my mommy I will keep on writing good and posting testimonies about you on the Internet, my name is Fred John from New York my mum was having HIV/AIDS for years... We try several hospital no solution then on i keep on searching for help for medicine before I could find solution to it i saw a block on how Dr Benson cured people, with herbal medicine in all kind of disease I couldn't believe not i decided to give him a trial by contacted him to confirm if its real guessed what? My mother got within a month after i have try several hospitals before no solution to my mom cancer before she finally got heal by Dr Benson, i am so happy now for the good work Dr Benson has to my family. Him also has herbal medicine to heal all these follow disease Such as HIV, DIABETES, ASTHMA, HPV, HERPES HEPATITIS SYPHILIS BACTERIA CANCER please don't hesitant to Dr Noble contact him on the following email drbenson52@gmail.com" or whats-app Dr Benson..on the following number +2348141972381 for Herbal medicine The only trusted and tested herbal medicine.. Dr lets put heads together to fight all kind of disease by sharing this awareness...

    ReplyDelete
  12. Are you paying $189 a week for Valtrex or $67 for Acyclovir to suppress your outbreaks? Have you considered your yearly prescription costs for these drugs, $2000+ a year! Anyone who has herpes can attest to the painful and embarrassing symptoms. Unfortunately, many find that doctor recommended products are frequently not effective at taking care of the problem.DR OHIKHOBO herbal remedy will get to the root of the cause and cure you completely rather than suppress outbreaks with medication. and leave you happier, healthier, and outbreak FREE!.let my tell you all how i was cured completely from herpes.at first i never believed i could be cure considering all type of of medication i have been using but it all came like dream come true for me that i was able to be cured by DR OHIKHOBO herbal remedy.as i speak now I have no more outbreaks,.It could change your life.contact DR OHIKHOBO at drohikhoboherbalcenter@gmail.com or you can reach him through his whatssap at +2348103601042

    ReplyDelete
  13. I was cured of HIV with the used of natural herbs. My name is celina jolly and am from US. I love herbs so much. Most times, injection and drugs are just a waste of time. I was cured 8months ago, i suffered from HIV for 13yrs but with the help of Dr.Ogun herbal medicine, i was cured within few weeks of drinking the herbs he sent to me through courier delivery service. This same doctor also cured my Aunty from herpes, as soon as i heard she had herpes, i quickly refer her to Dr. Ogun and she was cured too after drinking his herbs.I have referred more than 15 persons to Dr.Ogun and they were all cured from their various illness. Have you taken herbs before?. You have spent so much money on drugs,injections,surgeries etc and yet you have no good result to show for it. Contact Dr.Ogun now, he is a herbalist doctor, i assured you of a cure if you drink his natural herbs. Dr.Ogun have herbs that cures Hiv, Herpes, diabetics, asthma, hepatitis, HBP, STD, cancer, chronic, etc. Contact Dr ogun through his Email address on:drogun62@gmail.com or WHATSAP/CALL him on +2348104991149 . Please share the good news to other people once you are cured

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  14. Hello, am Tanya Albert from United State. am happy sharing this great testimony on how i was checking for solution in the internet then miraculously i came Across Dr Ekpiku, the powerful herbalist that Cure Numerous individuals HSV-1 AND HSV-2 INFECTION,then i contacted his Email: (ekpikuspellhomeofgrace@gmail.com) I Explained everything to him and he prepared me a herbal medicine that cure my HSV-1 AND HSV-2 Disease totally after making use his herbal medicine, So My friends viewers why wait and be suffer when there is someone like Dr Ekpiku, that can cure any disease HIV/ CANCER/ HEPATITIS B VIRUS,LOW SPERM COUNT,ALS, ANCE PIMPUS, LUPUS VIRUS, You Can "CONTACT him Via : Email : (ekpikuspellhomeofgrace@hotmail.com) or Whats app; +2348073673757 You Can Contact Him Today And Get Your Problem Solved or call/text me +16506538578.

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  15. My son once had the problem of HIV/AID which affected his Education for years,i gave him different medication but there was no solution,i search the net and i found the contact of a doctor,who help me with his product on curing HIV/AIDS, CANCER< HERPES, HEP B, DIABITIES, GERNITAL WARTS, HPV, EPILEPSY problem and other deadly diseases,he also assured me that it is a permanent cure,my son took the medication for just 2 weeks and he was back to normal. for two years now he has been doing fine.I give all thanks to Dr Uwenbo for helping me out of such problem now am the hapiest person on earth for seeing my son doing better again.you can also contact him on dr.uwenboherbalhome@gmail.com, druwenboherbalhome@outlook.com. you can also call or whatsapp on +2349052309005 and get the product.

    ReplyDelete
  16. REAL CURE FOR GENITAL HERPES, HIV/AIDS, CANCER, DIABETES, HEPATITIS B, VAGINAL AND ITCHING BURNING, WITH PROVE..

    THE ONLY TRUE HERBALIST MAN WITH TEST RESULTS(PROVE) OF PEOPLE HE HAVE CURED OF MANY INFECTIONS AND DISEASES, AFTER CONTACTING 3 HERBALIST ONLINE, BUT ONLY HIM COULD CURE ME OF 2 YEARS GENITAL HERPES...HE IS REAL AND GENUINE. HIS PHONE NUMBER IS: +2348078467513 AND THIS IS HIS EMAIL: herbal.home247@yahoo.com

    I am Grace Clark by names from USA, I was diagnosed of herpes in 2015 and I tried all possible means to get cure but all to no avail until i saw a post in a health forum about herbal doctor called DR. OKUNS who prepare Herbal Medicine to cure all kind of diseases including herpes virus, at first i doubted if it was real, but i decided to give it a try, when i contact this herbal doctor via his email i bought the herpes herbal medicine from him and received it through DHL within 3 days and used it as prescribed, i tested negative within 2 weeks of usage. you can contact him via E-mail: herbal.home247@yahoo.com for any types of diseases solutions or WhatsApp/call him on: +2348078467513

    ReplyDelete


  17. I never thought i would be free from HERPES again after been diagnosed in 2010, i have tried everything possible in life from one hospital to another, series of tests, different kinds of medication, i had already lost hope until i meet Great testimonies online about drsebispelltemple@gmail.com , a specialist in herbal medication from Africa, i contacted him and he prepared HERPES herbal medication for me which i took for 7days and now i am completely cured. i want to use this medium to express my gratitude to him for saving my life and curing me from HERPES , for taking away all my pains and sorrows, I”m indeed grateful and i am so happy I”m now completly free from HERPES . i will continue to tell the good news of your great works to everyone, if you have HERPES, HIV/AIDS,ZIKA VIRUS,HPV or other disease contact him, Email: drsebispelltemple@gmail.com call or whatsApp him on +2348153863900 thank God for using dr sebi to save me from herpes virus . for more information contact me through my whatsapp number +17609739518.

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