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 a look at the new HSP 70 reps. The mechanical data still needs some better resolution. Hopefully teh 8-10 samples migh shed some light.
Next up is two more reps of PGEEP4.
Looks good, and given the doubling of reps we could easily drop ‘outlier’ runs and still have triplicates, tight triplicates.
GRB2… now good to go, with the first pair of reps dead on.
BMP2…. could use some help from the other mechanical stress runs
TLR….seemed like a relatively easy fix (besides no detection) in that just needed to correct for machine.
And the correction indicating the fact that expression was so low, only able to be detected by Opticon
The 8-15 runs had minimal control and temp samples with mechanical run in dups.
This needs a little carressing before integrating into data.
This should be in two columns with empty cells where no samples were run- in this order.
H_C_1 H_C_2 H_C_3 H_C_4 H_C_5 H_C_6 H_C_7 H_C_8 N_C_1 N_C_2 N_C_3 N_C_4 N_C_5 N_C_6 N_C_7 N_C_8 S_C_1 S_C_2 S_C_3 S_C_4 S_C_5 S_C_6 S_C_7 S_C_8 H_T_1 H_T_2 H_T_3 H_T_4 H_T_5 H_T_6 H_T_7 H_T_8 N_T_1 N_T_2 N_T_3 N_T_4 N_T_5 N_T_6 N_T_7 N_T_8 S_T_1 S_T_2 S_T_3 S_T_4 S_T_5 S_T_6 S_T_7 S_T_8 H_M_1 H_M_2 H_M_3 H_M_4 H_M_5 H_M_6 H_M_7 H_M_8 N_M_1 N_M_2 N_M_3 N_M_4 N_M_5 N_M_6 N_M_7 N_M_8 S_M_1 S_M_2 S_M_3 S_M_4 S_M_5 S_M_6 S_M_7 S_M_8
8-15 run update
Mechanical looks decent after correcting.
However taken together, bothersome the difference in crude expression levels.
Had some wet works issues
Assuming correction is correct- still a big differences in mechanincal here- could be real.
No correction required as these were run on cfx, downside is some reps are not detected that would have been picked up with Opticon.
Do not see be shift in expression of mechanical stressed.
Easy correction but skeptical of some very, very low Cts