This is what I just shared with my staff! Hope this helps to everyone working in the NGS field!
Above is a must have for working on the bead cleanup! The more bead you have (actually the bead itself doesn’t matter but the volume of PEG/NaCl that buffers the bead matters but I am just describing the PEG/NaCl buffer as ‘bead’ here) the smaller DNA you can bind. 1x is good to get rid of primer dimers (<100bp) which is mostly what we have to get rid of after PCR. But sometimes we also see adapter dimers which usually size around 120bp. To get rid of that, we have to lower the bead amount to 0.8x or 0.9x. The lower the volume of beads you add, the more you will lose your target fragment as well, so I change between 0.8x and 0.9x depending on the amount of your target (the more you have the more aggressive (i.e. the lower bead) you can go).0.6x binds things >400bp so this is often used to get rid of bigger fragment in ‘dual size selection’ setup. The supernatant after 0.6x contains <400bp and to there we add *final* 1x or 0.8x of beads to bind the <400bp fragment. 0.6x-1x dual size selection captures 100-400bp fragments and 0.6x-0.8x captures 200-400bp.e.g. 0.6x-1x dual size selection: Prepare your DNA in 100ul Tris (or Elution buffer from BioO etc), add 60ul of bead, wait 15min and transfer 160ul supernatant to a new well. Add 40ul of beads to this supernatant and wait 15min, pellet/wash the beads by EtOH and elute the DNA in x ul of Tris. You can cut everything to half if you want but you have to be careful watching the beads dried up as 20ul of beads can get dried up fast (unless you use 2x concentrated beads :).When we are sequencing long inserts e.g. 2X150, the dual size selection can be tweaked to 0.5x-0.7x to enrich bigger fragments.