bomb.bio | TimH | Activity https://bomb.bio/members/timh/activity/ Activity feed for TimH. Tue, 21 Apr 2026 20:24:12 +1200 https://buddypress.org/?v= en-US 30 hourly 2 833f0f6ba5e2d13b8b0503be65931070 TimH replied to the topic Sera-Mag SpeedBead in the forum Carboxyl Magnetic Beads https://bomb.bio/forums/topic/sera-mag-speedbead/#post-9718 Wed, 16 Mar 2022 00:58:55 +1200 Hi Bernardo – sorry for the slow reply – we haven’t done a huge amount of testing using the hydrophilic beads. Did you get any further with this? We have done plenty of NGS (Illumina mostly) using GITC and the hydrophobic Speedbeads  – it doesn’t appear to cause us issues….could you clarify if its an issue for you? As above, we usually only get…Read more

]]> 5102b40f536be670a6208cd862b30dcc TimH replied to the topic BOMB protocol #7.1 gDNA extraction in the forum gDNA https://bomb.bio/forums/topic/bomb-protocol-7-1-gdna-extraction/#post-9717 Wed, 16 Mar 2022 00:40:02 +1200 Hi Emily,

Blood does not really work that well with the 2:3:4 ratio, as there is a lot of liquid in there and (for humans/mammals) not many nucleated cells. You are probably better off going with a 2-step ’tissue’ protocol (#6.3), where you first protK treat in TNES, and then add in 1.5X GITC. From this point on it is basically 2:3:4.

Best…Read more

]]> 8eae6e636a289493ceff8e845e51c28a TimH replied to the topic BOMB protocol #4.2 Clean-up and size exclusion using carboxyl-coated MNPs in the forum Clean-up and size exclusion https://bomb.bio/forums/topic/4-1-bomb-clean-up-and-size-exclusion-using-carboxyl-coated-mnps/#post-9543 Thu, 03 Dec 2020 06:38:35 +1200 Hi Miriam – our group generally use deep well plates (1-2 mL) so when mixing using 1000 rpm on, for example, an eppendorf thermomixer, you won’t have to use seals at all.

Best wishes,

Tim

 

 

]]> 911f0d542971f84bdc2a21680a5e02d4 TimH replied to the topic BOMB protocol #6.4 TNA extraction from plants in the forum TNA https://bomb.bio/forums/topic/bomb-protocol-6-4-tna-extraction-from-plants/page/2/#post-9486 Sun, 12 Jul 2020 22:57:13 +1200 Hi Mike,

Sorry we are slow to the conversation, however, I think Phil has covered off the points I would say are important. Paramount is more stringent washing of beads – I strongly suspect the 230 peak is GITC contamination; especially as you point out you see it even when there is no plant tissue at all (so this is a general bead issue, not…Read more

]]> 4c259062dad9433971d25cb7bb1c0755 TimH replied to the topic buffer for particle resuspenssion in the forum COVID-19 https://bomb.bio/forums/topic/buffer-for-particle-resuspenssion/#post-9440 Tue, 30 Jun 2020 18:45:36 +1200 Hi Sheila – I would use TE – as Phil mentioned in your other post silica beads should work very similar to the carboylated ones we got the initial protocol optimised on. So keeping everything the same would be the best starting point. Best wishes, TimH

]]> 4ed5ff1ab8aaaf52073f175bd530e237 TimH 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-9374 Tue, 28 Apr 2020 21:40:19 +1200 You can find this information in protocol #6.1 on our main page, or find below in the poorly formatted copy/paste from this page. But chemicals of good quality sourced elsewhere will very likely be fine. (note, you have details of the beads already)

Ethanol (C2H6O, 99.9%) Honeywell/ Riedel-de Haёn 34963

Guanidine isothiocyanate (GITC, C2H6N4S)…Read more

]]> 2f92ab30e7397bf5053cab0ba74a943e TimH 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-9371 Tue, 28 Apr 2020 21:27:56 +1200 Hi OMC Healthcare – this bead works very well in our hands, but other beads are also likely to work well (including self-fabricated beads, as in our protocols). We’ve not detected any sign of PCR inhibitor – remember that the beads are washed in the preparation steps, and then go through purification involving more washes, before being resuspended…Read more

]]> ac1532f342883461651976019bed8c7f TimH 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-9318 Sun, 19 Apr 2020 08:22:51 +1200 Hi Emily – details for the beads used in the COVID protocol can be found at the bottom of the protocol page (GE Healthcare Sera-Mag Magnetic SpeedBeads Carboxylate-Modified Dia.: 1 μm; GEHE451521 05050250) along with details on their preparation.

We’ve not tested BOMB silica beads for SARS-CoV-2 yet, however, this will happen soon. In the…Read more

]]> e6e8a18a94a96d2e72638608057bcdb2 TimH 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-9280 Wed, 08 Apr 2020 01:52:57 +1200 Hi Alejandro – best of luck with your efforts. The anti-foam is an optional component as far as I am aware – it is the GITC and detergent that will lyse cells (and virus). So if you don’t have it, then you might want to still try without it.

We have not tried the V&P tool as in the video. I would think it is fine in principle, however, to avoid…Read more

]]> 74dc1a5c4eed7e7ccb358668f9f9050f TimH 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/#post-8993 Tue, 31 Mar 2020 20:42:47 +1200 Hi Bradley,

Many thanks for the message and sharing your protocol. Do you have a way to show/test inactivation of the virus? Commercial AVL is ineffective at inactivation of Ebola (https://journals.sagepub.com/doi/pdf/10.1177/1535676017703383), so please take this into consideration if/when you start working with actual virus. Be safe. You could…Read more

]]> 811a800b6b17e0559b9f737a8905cdcd TimH replied to the topic in the forum Adjusting BOMB protocol #8.1 for SARS-CoV-2 extraction https://bomb.bio/forums/reply/8980/#post-8987 Fri, 27 Mar 2020 01:35:55 +1200 Hi Alexander,

We are working with several facilities involved in virus testing to optimise modified BOMB protocols for RNA extraction that are both effective and safe. We will update on this as soon as we can, but we would like to underline our commitment to open science – precisely what is needed now when considering failing supply-chain and…Read more

]]> c816a54f78544a90f5a2a46fb79a47ad TimH replied to the topic BOMB protocol #7.1 gDNA extraction in the forum gDNA https://bomb.bio/forums/topic/bomb-protocol-7-1-gdna-extraction/#post-8927 Sun, 16 Feb 2020 01:04:40 +1200 Hi Jon – to prepare those beads for gDNA, RNA and TNA extraction take 1 mL of thoroughly resuspended bead mixture and place on a magnetic. Once beads have settled, remove the storage buffer (it contains sodium azide) and resuspend in 1 mL of TE buffer off the magnetic. Repeat process at least twice more and then resuspend in TE. We do this into 50…Read more

]]> 59a044049e617c19a74e6c4a32fb447b TimH replied to the topic BOMB protocol #5.1 plasmid DNA extraction from E.coli in the forum Plasmid Extraction https://bomb.bio/forums/topic/5-1-plasmid-dna-extraction-from-e-coli/#post-8777 Sun, 11 Aug 2019 08:04:03 +1200 Hi Sarah/Phil – just a quick message to confirm that for the TNA from tissues purification using Sera-Mag or BOMB beads; exactly the same protocol was used. As Phil mentioned, there was slightly higher yield for most tissues using BOMB beads…

Cheers,

Tim

]]> 62dd97266c86d458b289350cf0324463 TimH replied to the topic Sera-Mag SpeedBead in the forum Carboxyl Magnetic Beads https://bomb.bio/forums/topic/sera-mag-speedbead/#post-8540 Mon, 01 Jul 2019 04:59:41 +1200 .

]]> 07772bb7bf59f5fbdfe8263f162ba28b TimH replied to the topic Sera-Mag SpeedBead in the forum Carboxyl Magnetic Beads https://bomb.bio/forums/topic/sera-mag-speedbead/#post-8537 Sun, 30 Jun 2019 22:18:54 +1200 Hi Sebastian,

Many thanks for the detailed feedback. I have tried to split the two main challenges you raise so it is easier for others to follow. However, due to the common issue of clumping, I suspect the answer for both is the same (you need to more beads for capture, or less starting material):

PLASMID EXTRACTION

You are right, most of the…Read more

]]> a07bbc8e161fa09a8c469f44310c0cee TimH replied to the topic Sera-Mag SpeedBead in the forum Carboxyl Magnetic Beads https://bomb.bio/forums/topic/sera-mag-speedbead/#post-8533 Sun, 30 Jun 2019 08:44:36 +1200 Hi Sebastian,

 

Apologies for the slow reply here! The buffer the Speed Beads arrive in is not suitable for DNA handling – it contains Sodium Azide and is much too concentrated. What you need to do is take 1 mL of the resuspended beads as they arrive, wash 2 x in TE buffer (i.e. magnet, remove Aizde, resuspended in 1 mL TE, magnet, remove TE,…Read more

]]> 29e331ce3d23fea9d7b7e6e147f48da8 TimH replied to the topic BOMB protocol #6.4 TNA extraction from plants in the forum TNA https://bomb.bio/forums/topic/bomb-protocol-6-4-tna-extraction-from-plants/#post-2278 Wed, 12 Jun 2019 10:29:17 +1200 Hi Jstees – apologies for the slow reply! Yes, when adding GITC following TNES incubation (i.e. the DNA only tissue protocol) there is formation of precipitate, presumably SDS. Nevertheless, in our hands this clarifies at the isopropanol stage and does not appear to adversely affect purification. But please let us know if you find otherwise. Best…Read more

]]> b776554c5d29497ba381649940152771 TimH replied to the topic BOMB protocol #7.1 gDNA extraction in the forum gDNA https://bomb.bio/forums/topic/bomb-protocol-7-1-gdna-extraction/#post-2089 Wed, 09 Jan 2019 03:48:34 +1200 Hi AK Schilling – sorry for the slow reply – in case you are still wondering whether to give it a go: yes, people in my Department have tried BOMB on insects, following the Tissue extraction protocol as suggested by Tomek. I don’t think the chitin exoskeleton was broken down, but DNA was extracted all the same.

Cheers,

Tim

]]> 7a0d598e12ec4e9ca661c37d942d714b TimH replied to the topic Minipreps without centrifuge? in the forum Automation https://bomb.bio/forums/topic/minipreps-without-centrifuge/#post-1941 Thu, 13 Sep 2018 05:48:19 +1200 Hi Keoni – do you mean clearing the beads as in putting them on a magnet? Not really sure how to help as not familiar with the Zymo kit…as a suggestion, you might like to try our BOMB protocols for mini-prep….Your timing is good – we just released the paper on BioRxiv https://www.biorxiv.org/content/early/2018/09/12/414516

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