Submitted 4uL (108ng/uL) of mRNA from gigas gill (from DATE!; sometime in late August) to the Center for Array Technologies (CART) at UW. Sample was labelled “SR01″.
Results:
Results were received on 20090210. Comment from CAT staff member was that it looked “pretty good.” Here are links to the gel (look for SR01), the electoropherogram of SR01, and the EGRAM of the ladder.
Samples were pelleted and washed with 70% EtOH according to Ambion PolyA Purist protocol. Pellets were resuspended in 10uL of The RNA Storage Solution (included in the Ambion PolyA Purist Kit).
Results: The gill mRNA looks great! Good yield and good ratios. Hemocyte mRNA looks kinda rough and a very low yield (which was to be expected).
mRNA was isolated according to Ambion PolyA Purist protocol. After mixing samples with resin, samples were incubated @ RT for 1hr. Samples were washed per the protocol. However, the hemo sample was not clearing from the spin columns with the protocol-directed 3 min. spins. The column had to be spun up to 15 mins. in order for the column to clear. 
Results: The gill mRNA looks good (~1.8ug). The concentration of the hemo sample is extremely low and is below the error threshold for the NanoDrop, but it may not be that bad. The samples are in a relatively large volume (~200uL) and the yield is expected to be very small. So, I will precipitate these samples O/N @ -20C according to Ambion PolyA Purist protocol in order to concentrate them.
The two RNA samples from yesterday were precipitated and washed according to the Ambion PolyA Purist protocol and resuspended in 50uL of 0.1% DEPC-H2O.
Results: RNA readings look better than they did prior to precipitation. The hemo RNA samples will be combined with previous hemo RNA samples and mRNA will be isolated using the Ambion PolyA Purist Kit.
The 8 hemo samples were pooled and the 4 gonad/d.g. samples were pooled. RNA was isolated. The homo sample was resuspended in 100uL of 0.1%DEPC-H2O and the gonad/d.g. sample was resuspended in 50uL 0.1%DEPC-H2O. RNA was precipitated O/N @ -20C according to Ambion PolyA Purist protocol in preparation for mRNA isolation.
Hemos were collected from the remaining 12 clams as before and stored @ -80C. NOTE: 4 hemocyte samples were extremely cloudy. Possibly not hemos? Maybe gonad/d.g.? Gill tissue was collected from 5 clams and stored @ -80C.
RNA isolated on 20090116 was precipitated over the weekend @ -20C. Samples were treated according to Ambion PolyA Purist protocol and resuspended in 100uL of 0.1% DEPC-H2O. Samples were stored in the red “hard clam” box @ -80C.
Results: 260/280 look good for both gill and hemo samples. 260/230 looks OK for gill, but looks horrible (as usual) for hemos.
RNA was isolated from hard clam gill (0.08g; from 20090109) and from hard clam hemos (from 20090114). One “unknown” sample (from 20090114) was also processed. Pellets were resuspended in 50uL of 0.1%DEPC-H2O. Hemo samples were pooled. Samples were spec’d.
Results: 260/280 looks OK for hemos. The gill sample has excellent 260/280 and pretty good 260/230. Samples will be reprecipitated over the weekend @ -20C according to Ambion PolyA Purist protocol in preparation for mRNA isolation.
Bled 7 clams from 20090108 and 20090109. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and spun @ 100g for 30mins @ 4C. Most of the supe was removed, but left ~100uL in each tube to avoid disturbing any pellet. Samples were stored @ -80C in the red box with previous hard clam hemo samples.
NOTE: One sample was EXTREMELY cloudy. Likely not hemos.
Transferred supe to a fresh tube and added 1mL 70% EtOH to remaining pellet. Spun samples max speed @ 4C 30 mins. Removed supe and washed pellets with 1mL 70% EtOH. Spun max speed 10 mins. Removed supe . Resuspended the “supe” sample in 50uL 0.1%DEPC-H2O and the “pellet” sample in 100uL 0.1%DEPC-H2O.
Results: 260/280 ratios look good. The 260/230 ratios are still horrible. Total yield from these two samples are ~5ug. Will get more hemolymph from clams in order to use more total RNA in the mRNA isolation to maximize cost saving.
