bomb.bio | Alexander James Phillips | Activity https://bomb.bio/members/ajp1/activity/ Activity feed for Alexander James Phillips. Tue, 21 Apr 2026 20:24:12 +1200 https://buddypress.org/?v= en-US 30 hourly 2 256a25c270fd0bed2fd652c57547eb8a Alexander James Phillips replied to the topic Implementing BOMB protocol for RNA extraction in Colombia in the forum COVID-19 https://bomb.bio/forums/topic/implementing-bomb-protocol-for-rna-extraction-in-colombia/#post-9392 Tue, 19 May 2020 21:45:54 +1200 Alejandro and colleagues published their work.  I did a rough translation to English here.  They add Proteinase K to samples with blood.  They also have a different protocol (dilute with saline) for samples that have more mucus.  These links can also be found in the spreadsheet of Bomb.bio adopters / validators.

]]> d61df4ed270691fbf17c8a31425fe013 Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/page/2/#post-9384 Wed, 13 May 2020 12:35:54 +1200 <p dir=”auto”>== Technology adoption – who’s using what variant, where, for what ==</p>
<p dir=”auto”>Hi all,</p>
<p dir=”auto”>I went through the different forum posts to see who has said what and tried to guess where you’re all at with the Bomb.Bio protocol for RNA purification. Specifically I’m looking for:</p>
<p dir=”auto”>Technicians,…Read more

]]> 66bd9f777578ab4045dae3966c771c3b Alexander James Phillips replied to the topic Hillbilly Bead Viral RNA Extraction Protocol - BOMB Community in the forum COVID-19 https://bomb.bio/forums/topic/hillbilly-bead-viral-rna-extraction-protocol-bomb-community/page/2#post-9381 Mon, 11 May 2020 17:21:00 +1200 Hi Rachel,

If you want there’s a Bomb.Bio / OpenTrons RNA purification protocol from OpenCell here: https://github.com/UK-CoVid19/OpentronDev/blob/master/protocols/RNA%20Extraction%20MD%20V9.py
With accompanying doc here: https://docs.google.com/document/d/11Kfc2KW56N5ggyGUDIIb-YVgKA0DsH8MjnlfujjUXmc/edit

Give me a shout if you need…Read more

]]> 67bd2813e0bb85676d87bc6c6cea2275 Alexander James Phillips replied to the topic Implementing BOMB protocol for RNA extraction in Colombia in the forum COVID-19 https://bomb.bio/forums/topic/implementing-bomb-protocol-for-rna-extraction-in-colombia#post-9380 Mon, 11 May 2020 15:05:05 +1200 Hi Alejandro,

I don’t know if you got an answer to your question?:

higher RNA extraction efficiency can be achieved by adding the RNA binding buffer (protocol 8.2 with Gu-HCl)?

Regarding:

we plan to increase 50% and 100% the volume of beads in the protocol.

I know that TimH and TimM both suggested various approaches for increasing yields which…Read more

]]> c8a53c95537c2af7bc63e9930936f946 Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/page/2/#post-9333 Fri, 24 Apr 2020 12:42:08 +1200 Sorry I realised I forgot to give this feedback:

While GITC + detergent buffers are expected to inactivate coronaviruses (e.g. MERS-CoV, Kumar et al., 2015 https://www.ncbi.nlm.nih.gov/pubmed/26190637 ), this has not been definitively tested for SARS-CoV-2.

Note that Kumar et al. paper actually uses GITC (guanidinium isothiocyanate) containing AVL…Read more

]]> 8376f5d2bcc6b7d83bf077e7001cb13e Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/#post-9330 Thu, 23 Apr 2020 11:58:18 +1200 Hi Tim, I’ve contacted a few NHS labs in the UK reporting shortages of RNA extraction as well as posted on the UK DHSC crowd-sourcing ideas page ( https://testingmethods.crowdicity.com/post/3163640 ).  Being able to point to a peer reviewed publication would help to build credibility.  I’m going to reach out to CHL, is there anyone there you’d r…Read more

]]> f5cda04ac4d700c6805626a0cfe178a9 Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/#post-9329 Thu, 23 Apr 2020 08:04:47 +1200 The OpenCell team are really busy so I don’t know the full answer but they said “it was pretty immediate”.

mixed the IPA and beads by hand just before we started the run. He suspended the mixture manually so it was well mixed. Then, by the time the run started the beads were settled at the bottom of the well, and pipetting/mixing (which is the…

Read more

]]> adf207fbbc3626e9c9d882ab29a3e3fa Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/#post-9311 Thu, 16 Apr 2020 18:45:11 +1200 Another question / observation.  Protocol says: “NB, beads and isopropanol can be premixed to improve workflow” the team at OpenCell found the “beads congregate in the IPA and can’t easily be resuspended”.  Perhaps we should remove this note or qualify it with a “NB, beads and isopropanol can be premixed to improve workflow.  However test be…Read more

]]> aae0f3cf468de2f5139df249932a660d Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/#post-9308 Tue, 14 Apr 2020 09:58:27 +1200 Thank you Tim!  Points awarded for data and clarity.  Not for formatting and prettiness 😉 🙂

]]> 435e57b9d0437857305d9e222c3b667e Alexander James Phillips replied to the topic SARS-CoV-2 Purification (Viral Transfer Media) - BOMB extraction protocol in the forum COVID-19 https://bomb.bio/forums/topic/the-official-sars-cov-2-bomb-extraction-protocol/#post-9304 Mon, 13 Apr 2020 11:01:19 +1200 Will NZ Bomb.bio and Canterbury Health Laboratories teams publish a paper on the validation of the protocol?  Thank you for releasing the protocol so quickly.

]]> 34fb3accc86516b80446c9e927e09bad Alexander James Phillips replied to the topic in the forum Adjusting BOMB protocol #8.1 for SARS-CoV-2 extraction https://bomb.bio/forums/reply/8980/#post-8988 Fri, 27 Mar 2020 01:48:52 +1200 Thank you Tim.  Completely agree.  It’s an absolute honour to receive your message.  Please contact me if you are blocked by any specific IP as currently working with an amazing bunch of people pushing for something like: http://coronaopensource.org/licences

Done a BBC interview last week (11:45+) https://www.bbc.co.uk/sounds/play/w3csy7l6  and…Read more

]]> 0a2ff18d3417d81246dc8bae7352a219 Alexander James Phillips replied to the topic Adjusting BOMB protocol #8.1 for SARS-CoV-2 extraction in the forum COVID-19 https://bomb.bio/forums/topic/adjusting-bomb-protocol-8-1-for-sars-cov-2-extraction/#post-8980 Thu, 26 Mar 2020 11:44:16 +1200 Hi team,

I love your commitment to open science.  I’m co-founder of HelpfulEngineering.org (13,000+ volunteers against Covid-19).

Would a modified version be applicable to RNA extraction of Corona virus from samples from a human?  Presumably we’d change the protocol to remove Step 2 “Pellet the cells via centrifugation at 500g and discard t…Read more

]]> 6361baf16d238ffff45842c7ba818b5a Alexander James Phillips replied to the topic Silica bead morphology in the forum Silica Magnetic Beads https://bomb.bio/forums/topic/silica-bead-morphology/#post-8979 Thu, 26 Mar 2020 11:00:36 +1200 For others looking there was an answer given to this question here: https://bomb.bio/forums/topic/modified-stober-process/#post-8975

Eunhae, it would be good to hear whether this approach worked for you?

Kind regards,

AJP

]]> c8a5dc9f0b6b376dbd383fd5dade29e6 Alexander James Phillips became a registered member https://bomb.bio/activity/p/4461/ Thu, 26 Mar 2020 10:49:17 +1200 0