A few outliers remaining

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Integrating last bit of qPCR data into master datasheet. This includes 5 runs post 8/15. likely error above – second EF1 was 18s test. CARM Looks nice, corrected… Elong factor Correction is fine, but mechanical reps have some issues As noticed in last batch of analysis these need to be checked at raw data level… Read more »

Finishing out with the mechanical

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Currently there is a pretty robust spreadsheet and over the past few days Jake has cranked through some reps to see how the oysters that were mechanically stressed hold up. Below is how these data are integrated. Currently the 8-10 samples (yellow) have been skipped, but we might have a look. First up is having… Read more »

Dirty and crude with Oly qPCR

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Taking the most decent Ct values, I did the simple and crude calculation, normalizing with EF1 and looking at fold over minimum. Seems to be EF1 data is skewing. Will take a look with actin and also compare delta Ct, using this as a sound reference.

Passing Flanks

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A first look at population differences at qPCR primer sites for three population of Olympia oysters Plate 1 (samwhite_112381) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR primers. BMP2 Limited coverage CARM Better coverage conflicts were ambigs (ie S,W,R) HSPb11 Missed qPCR primer (R did not seem to… Read more »

Quick Carmalign

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The first batch of sequencing came into today to verify sequence of Olympia oyster qPCR primers. 1) imported .ab1 files into CLC, 2) trimmed “CARM” sequences 3) aligned to comp7220_c0_seq2

Shortish list

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In selecting qPCR targets from the Oly transcriptome (version 3) I came up with the following list. In general this was done by first focusing on stress response GO slim terms, followed by simple word searches. The table is available for download here The next step would be some joining & file converting to pull… Read more »