An Interview with Dr. Lindsay Parkes, Senior Research Scientist, Porvair Sciences
In the past decade there have been many advancements in ChIP assays please give an overview of Chromatrap’s ChIP Assay Technology and what improvements have been made?
The Chromatrap ChIP technology is a bead-free method of performing ChIP. The potential of the technology emerged from our capabilities in manufacturing porous plastic filters for the filtration and separation of biological materials. By functionalising the filter with capture proteins (eg. Pro-A, Pro-G), we identified a fresh new way of performing ChIP that eliminates the use of beads therefore overcoming the common challenges associated with these traditional ChIP assays.
Chromatrap continues to improve our technology and products in response to customers needs and changes in the market. Recently, we have made improvements to the sensitivity of the ChIP assay. Our uniquely orientated proteins ensure that every binding pocket is accessible to antibody-chromatin complexes thus maximizing capture efficiency. With researchers looking for more sensitive assays we push the development of our kits to not only be the best to use but deliver the highest sensitivity for a wide range of biological samples.
How does this compare to other standard ChIP assay technologies?
Unlike standard bead-based ChIP assays, Chromatrap uses a unique filter-based system for the capture and selective enrichment of DNA-associated binding proteins. By eliminating beads (magnetic and agarose) from our ChIP technology, we were able to develop a ChIP assay that is far easier, quicker, more robust and most importantly more sensitive than standard ChIP assays.
Why is it important to use a solid-state ChIP assay rather than a bead-based system? What are the advantages and limitations?
When it comes to ChIP assays, sensitivity is a key. Chromatrap uses our patented inert porous plastic material, Vyon. This significantly reduces the background noise often found in results from ChIP assays using magnetic or agarose beads, which can inherently attract non-specific binding and contribute to higher backround and masking of results.
From chromatin extraction to elution of sequencing-ready DNA, bead-based ChIP assays can take up to 5 days to complete. This can be done in as little as 5 hours using the Chromatrap system with it’s optimally oriented proteins and improved molecular mixing.
With Chromatrap, all steps are carried out in by centrifugation. This overcomes the problems with multiple pipetting steps and sample loss by retaining bound complexes on the filter until elution. Not only does this speed up the workflow but Chromatrap users benefit from its ease of use.
As with any commercial assay kit, user optimisation may be required. Our dedicated technical support team are always on hand to provide guidance and advice. Chromatrap provides all the reagents you need from chromatin extraction to IP to DNA purification.
What size samples can be used with Chromatrap ChIP assays? What are the applications of these assay sizes?
Chromatrap was developed to deliver a robust and highly sensitive kit compatible with a wide range of samples. ChIP can be perfomed from as little as 1000 cells or 50ng of tissue. The flexibility of the system means upto 50µg chromatin can be used per assay.
Chromatrap has the widest dynamic range of any available ChIP assay meaning it can be used for any application from precious clinical samples to abundant cell lines. In cases such as clinical labs, researchers may only have access to limited patient samples and therefore require a highly sensitive kit.
Downstream PCR and Next Generation Sequencing are common next steps for enriched chromatin, what advantages are there for Chromatrap’s ChIP assay over other commonly used methods?
The sensitivity of the Chromatrap ChIP assay allows detection of gene targets in qPCR from the lowest amount of starting material. Maximised capture of target antibody-DNA complexes on the Chromatrap columns and no sample loss allows amplification of even low abundant gene targets which may be undetectable with bead-based systems.
Using the Chromatrap system, complex sequencing data can be obtained from ChIP-seq of significantly lower amounts of starting material. The high yield of DNA from Chromatrap ChIP allows NGS sequencing from a single IP from as little as 1000 cells without any need for sample pooling. Higher input DNA improves NGS library complexity.
How can automation of ChIP assay protocols improve the quality, complexity and accuracy of research?
Automation of ChIP using a technology like Chromatrap’s allows accurate complex data to be obtained rapidly and without the risk of pipetting or handling errors. With this format, researchers can investigate multiple antibody and gene targets in parallel.
The Chromatrap technology is perfectly suited to high-throughput assays. Chromatrap 96 well plates contain a Protein-A or Protein-G functionalised filter in each of the 96 wells. Just like our standard column kits, the 96 well high-throughput products contain all the buffers and reagents you need to start and finish your assay. Precise well-to-well consistency allows accurate reproducible and repeatable results in every assay.
The Chromatrap® 96 HT system can also be set up for automated liquid handling providing an even faster and more efficient method for performing ChIP assays. Large, reliable data sets can be collected efficiently, enabling widespread effects to be studied across multiple samples and multiple cell types; all carried out simultaneously.
What impact can improved ChIP assay technology have on important research areas such as cancer and epigenetic research?
Epigenetics is a vital research area in the study of health. Modifications which do not cause a change in the underlying DNA sequence are of particular interest in pathologies such as cancer due to their reversible nature. ChIP is the most powerful tool in understanding the interactions of histones and transcription factors with target DNA which illicit key signalling responses. Epigenetic drugs, such as HDAC inhibitors, have been growing in popularity in the treatment of cancers and their effects are often tested in ChIP.
Having the most sensitive information about the effects, both on and off target, of these drugs can only help improve health outcomes in the long term. Faster, more sensitive and reproducible ChIP assays allow higher throughput research into the mechanisms underlying diseases and testing of their treatments.
What is the future of ChIP assay technology, and for Chromatrap?
Incremental improvements to the assay and workflow. Compatibility of the assay with downstream applications. Chromatrap – adapting the unique technology and its benefits for other or downstream life science applications.
With increasing focus on epigenetic factors in health research and treatment, ChIP will continue to grow in popularity. Technologies will inevitably need to improve in sensitivity, efficiency and throughput to accelerate this research. Chromatrap will maintain its position at the forefront of ChIP technology while developing our system to ensure it always deliver more efficient, sensitive and simple ChIP assays for chromatin from a wide variety of sources. We will continue to adapt the the technology, already compatible with a wide range of downsteam processes, to emerging analytical techniques.
The success of Chromatrap in ChIP and the unique advantages it provides over bead-based assays presents exciting opportunities for the technology in a broad range of applications. Our team are adapting the novel solid-state platform for established and emerging epigenetic and biological enrichment techniques so that more researchers can benefit from its many advantages and focus on the bigger questions in their research.
Where can readers find more information?
Visit www.chromatrap.com to find out more about Chromatrap, recent publications, application notes and product information.
About Dr. Lindsay Parkes
Dr. Lindsay Parkes is the lead scientist in the R&D of novel and existing technologies at Porvair Sciences. Her primary focus is to develop the unique materials manufactured at Porvair Sciences into innovative products and applications for life science and medical research.
After starting her career as a bacterial geneticist at Swansea University, Lindsay was awarded a PhD in Molecular Biology and Genetics. To follow her interest in molecular biology in academic research, Lindsay continued with a postdoctoral role in testing the efficacy of key antimicrobial drugs. During her research, Dr. Parkes became involved in a collaborative industry academic project with Porvair on the research and development of Chromatrap products.
Working with Porvair Sciences has provided Dr. Lindsay Parkes with the perfect opportunity to establish a challenging and exciting career combining her passion for research and interest in product development.
Sponsored Content Policy: News-Medical.net publishes articles and related content that may be derived from sources where we have existing commercial relationships, provided such content adds value to the core editorial ethos of News-Medical.Net which is to educate and inform site visitors interested in medical research, science, medical devices and treatments.
"Lindsay Parkes, Mtafiti Mtendaji wa Sayansi ya Porvair, alisema: ""Kwa miaka kumi iliyopita, kumekuwa na maendeleo mengi katika vipimo vya ChIP, tafadhali toa muhtasari wa teknolojia ya Chromatography ya ChIP na ni maboresho gani yamefanywa." Chrometrap ChIP ni njia ya kuunda chapa ya chapa ya chapa ya chapa ya chapa ya chapa. Uwezo wa teknolojia hiyo ulitokana na uwezo wetu wa kutengeneza vichungi vya plastiki vyenye madoadoadoa kwa ajili ya kuchuja na kutenganisha vifaa vya kibiolojia. Kwa functionalising kichujio na protini kukamata (kwa mfano. "Pro-A, Pro-G, na ""Njia mpya ya kufanya ChIP ambayo huondoa matumizi ya shanga, hivyo kushinda changamoto za kawaida zinazohusiana na vipimo hivi vya jadi vya ChIP.""" Chrometrap inaendelea kuboresha teknolojia yetu na bidhaa kwa kukabiliana na mahitaji ya wateja na mabadiliko katika soko. Hivi karibuni, tumefanya maboresho kwa unyeti wa kipimo cha ChIP. Protini zetu za kipekee zinazohitajika kuhakikisha kwamba kila mfuko wa kuunganisha unapatikana kwa misombo ya antibody-chromatin hivyo kuongeza ufanisi wa kukamata. Kwa watafiti wanaotafuta vipimo nyeti zaidi, tunasukuma maendeleo ya vifaa vyetu kuwa sio tu bora kutumia, lakini kutoa unyeti wa juu zaidi kwa sampuli mbalimbali za kibiolojia. Jinsi gani hii inalingana na teknolojia nyingine za kawaida za kipimo cha ChIP? Tofauti na vipimo vya kawaida vya ChIP, Chromatrap hutumia mfumo wa kipekee wa kuchuja kwa ajili ya kukamata na kuimarisha kwa kuchagua protini za kuunganisha zinazohusiana na DNA. Kwa kuondoa shanga (magnetic na agarose) kutoka kwa teknolojia yetu ya ChIP, tuliweza kuendeleza kipimo cha ChIP ambacho ni rahisi zaidi, haraka zaidi, imara zaidi na muhimu zaidi kuliko vipimo vya kawaida vya ChIP. Kwa nini ni muhimu kutumia chombo cha kugundua chembe za msingi badala ya chombo cha kugundua chembe za msingi? Kuna faida na mapungufu gani? Kwa ajili ya vipimo vya ChIP, unyeti ni muhimu. Chromatrap hutumia nyenzo yetu ya plastiki yenye madoadoadoa, Vyon. Hii hupunguza kwa kiasi kikubwa kelele ya nyuma ambayo mara nyingi hupatikana katika matokeo ya vipimo vya ChIP kwa kutumia shanga za sumaku au agarose, ambazo zinaweza kuvutia kuunganisha isiyo ya kawaida na kuchangia nyuma ya juu na kuficha matokeo. Kutoka kwa uchimbaji wa chromatin hadi kuondolewa kwa DNA iliyo tayari kwa mfuatano, vipimo vya ChIP vinavyotegemea beads vinaweza kuchukua hadi siku tano kukamilika. Hii inaweza kufanyika katika muda mfupi kama saa tano kwa kutumia Chromatrap mfumo na ni vyema oriented protini na kuboreshwa molekuli kuchanganya. Pamoja Chromatrap, hatua zote ni kufanyika katika kwa centrifugation. Hii inashinda matatizo na hatua nyingi pipetting na sampuli hasara kwa kudumisha complexes amefungwa juu ya chujio mpaka elution. Si tu kwamba hii kuharakisha mtiririko wa kazi lakini watumiaji Chromatrap kufaidika na urahisi wake wa matumizi. Kama ilivyo na kit yoyote ya majaribio ya kibiashara, optimization ya mtumiaji inaweza kuhitajika. Timu yetu ya msaada wa kiufundi imejitolea daima kwa mkono kutoa mwongozo na ushauri. Chromatography inatoa vifaa vyote vya kuondoa chromatin na kuondoa DNA. Ni aina gani ya sampuli za Chromatrix zinapaswa kutumiwa? Ni nini matumizi ya ukubwa huu wa uchunguzi? Chromatrap ilitengenezwa kutoa kit thabiti na nyeti sana sambamba na aina mbalimbali ya sampuli. ChIP inaweza kutengenezwa kutoka kwa seli chache kama 1,000 au 50ng ya tishu. Kwa sababu ya uwezo wake wa kubadilika, hadi 50mg ya chromatin inaweza kutumika kwa kila kipimo. Chromatrop ina mbalimbali pana ya nguvu ya yoyote chapa chapa, maana inaweza kutumika kwa ajili ya maombi yoyote kutoka sampuli ya thamani ya kliniki kwa mistari ya seli nyingi. Katika kesi kama vile maabara ya kliniki, watafiti wanaweza tu kuwa na upatikanaji wa sampuli ndogo za mgonjwa na kwa hivyo wanahitaji kit nyeti sana. PCR ya chini ya mtiririko na mfuatano wa kizazi kijacho ni hatua za kawaida za chromatin iliyotajwa, ni faida gani za Chromatrap's ChIP assay juu ya mbinu zingine zinazotumiwa kwa kawaida? Chromatography ChIP ni njia ya uchunguzi wa chembe za urithi za chembe za urithi zinazotumiwa katika qPCR. Utafiti wa juu wa targets ya antibody-DNA complexes kwenye safu za Chromatrap na hakuna hasara ya sampuli inaruhusu kupanua hata targets za chini za wingi wa jeni ambazo zinaweza kuwa hazina kuonekana na mifumo ya bead-based. Kwa kutumia Chrometrap, data ngumu ya mfululizo inaweza kupatikana kutoka kwa ChIP-seq ya kiasi kidogo cha nyenzo ya kuanza. Kwa sababu ya uwezo wa DNA ya Chromatrop, chapa ya NGS inaweza kuunganisha chembe za DNA kutoka kwa chembe za DNA za chembe za DNA za chembe za DNA za chembe za DNA za chembe za DNA za chembe za DNA za chembe za DNA. DNA ya juu ya pembejeo inaboresha utata wa maktaba ya NGS. Jinsi gani automatisering ya ChIPs inaweza kuboresha ubora, utata na usahihi wa utafiti? Automation ya ChIP kutumia teknolojia kama Chromatrap inaruhusu data sahihi tata kupatikana kwa haraka na bila hatari ya pipetting au makosa ya utunzaji. Kwa njia hiyo, watafiti wanaweza kuchunguza viungo vingi vya kinga na chembe za urithi kwa wakati mmoja. Teknolojia ya Chromatrap inafaa kikamilifu kwa vipimo vya high-throughput. Chromatrix 96 ina filters ya protini A na protini G katika kila moja ya visima 96 Kama vile vifurushi vyetu vya kawaida vya safu, bidhaa za 96-well zenye utoaji wa juu zina buffers na reagents zote unazohitaji kuanza na kumaliza kipimo chako. Usahihi vizuri-kwa-bora uthabiti inaruhusu sahihi reproducible na repeatable matokeo katika kila kipimo. Chromatrix 96HTP inaweza pia kuundwa kwa ajili ya automatiska ya kuhamisha kioevu, kutoa njia hata kwa kasi zaidi na ufanisi zaidi kwa ajili ya kufanya vipimo ChIP. Mkusanyiko mkubwa wa data ya kuaminika inaweza kukusanywa kwa ufanisi, kuwezesha athari za kuenea kuchunguzwa katika sampuli nyingi na aina nyingi za seli; zote zinafanywa kwa wakati mmoja. Utafiti wa ChIP unaonyesha kuwa kuna uwezekano mkubwa wa kuathiri utafiti wa epigenetic. Epigenetics ni eneo muhimu la utafiti katika utafiti wa afya. Mabadiliko ambayo hayasababishi mabadiliko katika mfululizo wa msingi wa DNA ni ya kuvutia hasa katika pathologies kama vile kansa kutokana na asili yao reversible. ChIP ni chombo chenye nguvu zaidi katika kuelewa mwingiliano wa histones na sababu za maandishi na DNA ya lengo ambayo huficha majibu ya ishara muhimu. Dawa za epigenetic, kama vile inhibitors HDAC, zimekuwa zikiongezeka katika umaarufu katika matibabu ya kansa na athari zao mara nyingi zinajaribiwa katika ChIP. Kuwa na habari nyeti zaidi kuhusu athari, zote mbili kwenye na nje ya lengo, za dawa hizi zinaweza tu kusaidia kuboresha matokeo ya afya kwa muda mrefu. Uchunguzi wa haraka, nyeti na reproducible wa ChIP huwezesha utafiti wa juu wa utaratibu wa magonjwa na upimaji wa matibabu yao. Nini ni maendeleo ya teknolojia ya ChIP na Chromatrix? Uboreshaji wa kuongezeka kwa vipimo na mtiririko wa kazi. Upatanaji wa kipimo na maombi ya chini ya mtiririko. Chromatrap <unk> kurekebisha teknolojia ya kipekee na faida zake kwa ajili ya maombi mengine au chini ya sayansi ya maisha. Kwa kuzingatia zaidi na zaidi sababu za epigenetic katika utafiti wa afya na matibabu, ChIP itaendelea kukua katika umaarufu. Teknolojia bila shaka itahitaji kuboresha katika unyeti, ufanisi na throughput kuharakisha utafiti huu. Chrometrap itaendelea nafasi yake katika mstari wa mbele wa teknolojia ya ChIP wakati wa kuendeleza mfumo wetu kuhakikisha daima kutoa vipimo vya ChIP bora, nyeti na rahisi kwa chromatin kutoka vyanzo mbalimbali. Sisi kuendelea kurekebisha teknolojia, tayari sambamba na mbalimbali ya downstream michakato, kwa mbinu zinazoibuka uchambuzi. Mafanikio ya Chrometrap katika ChIP na faida za kipekee zinazotoa juu ya vipimo vya msingi wa bead zinaonyesha fursa za kusisimua kwa teknolojia katika aina mbalimbali za maombi. Timu yetu inabadilisha jukwaa la hali ngumu la riwaya kwa mbinu za utajiri wa epigenetic na biolojia zilizowekwa na zinazoibuka ili watafiti zaidi waweze kufaidika na faida zake nyingi na kuzingatia maswali makubwa katika utafiti wao. Wasomaji wanaweza kupata wapi habari zaidi? Kwa mfano, unaweza kutembelea tovuti ya Chromatrix kwa maelezo ya ziada kuhusu Chromatrix, na kwa maelezo ya ziada kuhusu Chromatrix. Lindsay Parkes ni mwanasayansi wa kuongoza katika R&D ya teknolojia mpya na zilizopo katika Sayansi ya Porvair. Lengo lake kuu ni kuendeleza vifaa vya kipekee vilivyotengenezwa katika Sayansi ya Porvair katika bidhaa za ubunifu na matumizi kwa sayansi ya maisha na utafiti wa matibabu. Baada ya kuanza kazi yake kama mtaalamu wa maumbile ya bakteria katika Chuo Kikuu cha Swansea, Lindsay alipewa PhD katika Biolojia ya Molekuli na Genetics. Alipoanza kufanya utafiti wa molekuli, Lindsay alijiunga na utafiti wa postdoctoral katika utafiti wa ufanisi wa dawa muhimu za antimicrobial. Wakati wa utafiti wake, Dk Parkes alijihusisha na mradi wa kitaaluma wa ushirikiano na Porvair juu ya utafiti na maendeleo ya bidhaa za Chrometrap. Kufanya kazi na Porvair Sayansi imempa Dk Lindsay Parkes fursa kamili ya kuanzisha kazi ngumu na ya kuvutia inayochanganya shauku yake ya utafiti na maslahi katika maendeleo ya bidhaa. "Sheria ya maudhui ya udhamini: ""News.Medical.net kuchapisha makala na maudhui yanayohusiana ambayo inaweza kuwa inayotokana na vyanzo ambapo tuna uhusiano wa kibiashara, ikiwa maudhui kama hayo huongeza thamani kwa maadili ya msingi ya uhariri wa News.Medical.Net ambayo ni kuelimisha na kuwajulisha wageni wa tovuti wanaopendezwa na utafiti wa matibabu, sayansi, vifaa vya matibabu na matibabu."