I am trying to plasmid prep the entire library and am getting low yields. Any suggestions?

Opinion #1 - If you are growing these for the purpose of a plasmid prep, you may want to extend the incubation time to 20 hours. You MUST shake/incubate with microporous seals to achieve good growth. Also, we inoculate in house two deepwell plates for each and combine the two blocks to double the DNA. For instance, we inoculate plate SH2001 into two blocks, spin for a pellet, resuspend, and combine the two blocks. Opinion #2 - Since the most important things are good aeration (at least 200rpm's in a shaker adapted for bioblocks so they do not cross contaminate), breathable plate seals, no glycerol in the media, then depending on the size of their bioblock you may be able to use 1.4mls per block, and incubate ~20hrs. We believe this will give an average OD600 of about 0.5 To increase the OD and yields you can combine the pellets of two blocks and prep together and/or you might try to stamp the plates onto LB agar containing antibiotic and then use the colonies to inoculate the bioblocks rather than going from the glycerol stock plate directly (would be fresher growth rather than coming out of a freeze state).