Announcement

Collapse

Welcome to the New Seqanswers!

Welcome to the new Seqanswers! We'd love your feedback, please post any you have to this topic: New Seqanswers Feedback.
See more
See less

AMPure XP vs SPRI beads

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • AMPure XP vs SPRI beads

    Hey guys

    Curious as to which system you think is better? I've been trawling this forum regarding size selection using magnetic beads, for use in RADseq (a modified gDNA illumina prep). I'm just a little confused -

    - can you buy SPRI beads separately from the technology/hardware? I can't find anything on the beckman page for just SPRI beads. Or am I being dumb and the beads rely on the hardware to work, so you have to buy the whole system for automated library prep?

    - are AMPure XP beads (which I have access to) just as good at size selection as SPRI beads? I'm hearing a lot more about the SPRI system on this forum for size selection, rather than the XP beads.

    Ideally I would like to size select for fragments 300-500bp, for which I'm aware I'll probably need to do a double selection (one to eradiate fragments >500bp, the other to eradicate fragments <300bp), which is fine.

    Also, if anyone knows a good method to calculate the beadNA ratio other than trial and error, that would be greatly appreciated!

    Cheers

    Tali

  • #2
    Ampure XP beads are SPRI beads. It is easy to test on a ladder, or look at the metagenomics paper in PloS one for the ratios.

    Comment


    • #3
      Ahh ok, I hadn't realised that! I'll try out a couple of ratios (based on that paper, thanks for that reference) on a ladder.

      Thanks a lot

      Comment


      • #4
        Originally posted by Chipper View Post
        Ampure XP beads are SPRI beads. It is easy to test on a ladder, or look at the metagenomics paper in PloS one for the ratios.
        I need the complete information of "the metagenomics paper in PloS one ". Thanks.

        Comment


        • #5
          Originally posted by Tali7 View Post
          Ahh ok, I hadn't realised that! I'll try out a couple of ratios (based on that paper, thanks for that reference) on a ladder.

          Thanks a lot
          I want to know your result about the ratios. Thanks.

          Comment


          • #6
            Hi Tali,
            You are correct that the website is a little confusing! Our SPRI products are on the Beckman Coulter Genomics website. Here is a link directly through to the AMPure XP page.

            https://www.beckmancoulter.com/wsrpo...tion/index.htm

            If you have any further questions or queries then do not hesitate to get in touch.

            Best wishes

            Comment


            • #7
              Hi,

              Thank you! I have the SPRI bead. I will use it to select PCR product of 300-500bp size. I use the recommend protocal but the cut-off is not clear. On the website I can not find any information. Can you help me?

              Comment


              • #8
                your link still is confusing

                hi, your link is wrong, there's no product information.
                I'm just wondering if there is a way to search in your company website!
                Originally posted by Ber7702 View Post
                Hi Tali,
                You are correct that the website is a little confusing! Our SPRI products are on the Beckman Coulter Genomics website. Here is a link directly through to the AMPure XP page.

                https://www.beckmancoulter.com/wsrpo...tion/index.htm

                If you have any further questions or queries then do not hesitate to get in touch.

                Best wishes

                Comment


                • #9
                  Dear LucyYang1991,
                  That is strange, I just clicked the link and it took me directly to the AMPureXP page. If it is your first time to the website, you may need to select your region and it should then take you to the product page.

                  You could try this link to our Life Sciences page.

                  https://www.beckmancoulter.com/wsrpo...very/index.htm

                  There is a small magnifying glass in the top right. Click on that to bring up the search bar.

                  Comment


                  • #10
                    Apologies, I was not notified that you had responded to my link. I realise this is now a very late reply but the cut off is around 120-150bp when using the standard x1.8 ratio.

                    It is not a sharp cutoff. You will still get some products smaller than the cutoff but with significantly reduced amounts. Below 100bp or so all the fragments will be removed.

                    Originally posted by xiaoyuan zi View Post
                    Hi,

                    Thank you! I have the SPRI bead. I will use it to select PCR product of 300-500bp size. I use the recommend protocal but the cut-off is not clear. On the website I can not find any information. Can you help me?

                    Comment


                    • #11
                      OK, thanks a lot, this is the first time to the website. Maybe that's the problem here.
                      Originally posted by Ber7702 View Post
                      Dear LucyYang1991,
                      That is strange, I just clicked the link and it took me directly to the AMPureXP page. If it is your first time to the website, you may need to select your region and it should then take you to the product page.

                      You could try this link to our Life Sciences page.

                      https://www.beckmancoulter.com/wsrpo...very/index.htm

                      There is a small magnifying glass in the top right. Click on that to bring up the search bar.

                      Comment


                      • #12
                        Originally posted by Chipper View Post
                        Ampure XP beads are SPRI beads. It is easy to test on a ladder, or look at the metagenomics paper in PloS one for the ratios.
                        hi
                        i am testing the ampure beads to see is it working or not on a ladder DNA but i got band in 100 pb and i did not understand it can you see my attached image!
                        how do we know if the Ampure beads working or not ?

                        thank you very much.
                        comparing beads 11.7.17.jpg

                        Comment


                        • #13
                          Originally posted by hssalgh2 View Post
                          hi
                          i am testing the ampure beads to see is it working or not on a ladder DNA but i got band in 100 pb and i did not understand it can you see my attached image!
                          how do we know if the Ampure beads working or not ?

                          thank you very much.
                          [ATTACH]4827[/ATTACH]
                          We would need to know what the conditions of your test were and which lanes correspond to which treatment before we could really answer your question. Could you tell us these things?

                          Also, from what I understand, it's better to test the beads on enzyme-digested lambda-DNA (to generate a known fragment size profile) rather than on pre-packaged DNA ladder. Something about an ingredient inhibiting binding/elution (I'm fuzzy on the details). This may or may not be true, however, so take it with a grain of salt.

                          Comment


                          • #14
                            Originally posted by Carcharodon View Post
                            We would need to know what the conditions of your test were and which lanes correspond to which treatment before we could really answer your question. Could you tell us these things?

                            Also, from what I understand, it's better to test the beads on enzyme-digested lambda-DNA (to generate a known fragment size profile) rather than on pre-packaged DNA ladder. Something about an ingredient inhibiting binding/elution (I'm fuzzy on the details). This may or may not be true, however, so take it with a grain of salt.
                            Thanks for your reply and please see the attached Protocol that I had used for
                            Testing beads.
                            I use 2 microliter of ladder DNA diluted with 18 microliter of dearer and I add 36 microliter of beads then I complete the steps that in the attached file.
                            Many thanks
                            Attached Files

                            Comment


                            • #15
                              Originally posted by hssalgh2 View Post
                              Thanks for your reply and please see the attached Protocol that I had used for
                              Testing beads.
                              I use 2 microliter of ladder DNA diluted with 18 microliter of dearer and I add 36 microliter of beads then I complete the steps that in the attached file.
                              Many thanks
                              I see! Well, I'd recommend using a ratio slightly less than 1.8x. I'd lower that to 1.5x or so and see if it makes a difference (30 uL AmpureXP to 20 uL ladder dilution).

                              Comment

                              Working...
                              X