Author Archives: kubu4

qPCR – DNased Abalone Dg RNA from 20090625

Ran qPCR on DNased Abalone Dg RNA (07:12 Set), gDNA (06:50-10) and clean cDNA (from 20090422) using primers (H.crach_h-1fg_intron_Fw/Rv) designed to bind only to a region in an intron of the H.cracherodii hemocyanin gene. PCR setup/plate layout is here. Anneal temp of 50C was used.

Results: No PCR products in any samples, not even the positive control. It seems that the primers don’t work. Will design new primers, probably from a different species of abalone since there was essentially only one gene in H.cracherodii that had any intron sequence available..

gDNA Isolation – Dungan isolate MIE-14v

Cells stored in EtOH were pelleted 5000g, 10mins, 25C. A brownish smear was present along the inside of the tube after spinning; not really a pellet per se. Supe was removed and cells were washed twice with 1X PBS. The smear was reduced to a pellet after the first wash in PBS. The second wash resulted in a slightly smaller pellet, but a pellet was present nonetheless before proceeding. Cells were subjected to an enzymatic lysis in 180uL of a TE/Triton X-100/lysozyme mixture as described in the Qiagen DNeasy Kit for Gram-Positive Bacteria (and for cells having substantial cell walls). Cells were incubated in this mixture for 30mins @ 37C. 25uL of proteinase K and 200uL of Buffer AL were then added and the mixture was incubated @ 70C for 30mins. Protocol then followed the “normal” steps for isolation of gDNA. Sample was eluted in 100uL of Buffer AE and then spec’d.

Results: Well, it doesn’t look like there is any DNA at all… Will try precipitating the sample and bringing up the DNA (if there’s any) in a small volume. It should be noted that I spec’d these samples using the “RNA” setting, so the constant for concentration calcs is wrong (40), but doing quick math using the DNA constant (50) shows that there’s still almost nothing there…

qPCR – MV hemocyte cDNA from 20090614

Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically for the 18s runs:

3326A13

2100B07

3219A06

2100B15

3326A11

2100B12

2100A03

Plate layout/PCR set up is here. This is a second rep of these samples.

Results: Waters are clean. However, the following samples still are negative for an 18s amplicon:

Spec Reading – C.pugetti gDNA from 20090526

A recent email from JGI indicates that they are satisfied with the quality of DNA (as seen on 20090601), however their estimate of the gDNA concentration (42ng/uL) means that we have ~16ug of DNA. They requested 50ug. Based on the gel, their calculations are reasonable. However, the NanoDrop suggests that are sample is ~1350ng/uL! So, I’ve respec’d the sample and did a few dilutions to see how it looked.

Results: The undiluted sample is approximately the same concentration as initially reported. A 1:1 dilution produces the expected concentration of half the undiluted. The 1:10 and 1:100 dilutions deviate a bit from the expected concentrations, but are reasonably close. I still don’t know how to explain the discrepancy between what the gel analysis suggests vs. the NanoDrop spectrophotometric data.

qPCR – MV hemocyte cDNA from 20090614

Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically for the 18s runs:

3326A13

2100B07

3219A06

2100B15

3326A11

2100B12

2100A03

Plate layout/PCR set up is here.

Results: Waters are clean. However, the following samples still are negative for an 18s amplicon: