Geoduck Tissue Homogenization for NGS

20160901-20160912 Homogenization of juvenile geoduck samples for use in nucleic acid extractions

Processed samples saved in RNA later and those saved at -80 by grinding the tissues to a powder as described. Tissue Homogenization for Nucleic Acid Analysis Protocol

Sample list 20160901

EPI-250
EPI-251
EPI-257
EPI-258
EPI-264
EPI-265
EPI-271
EPI-271
EPI-272

Sample list 20160902

EPI-226
EPI-227
EPI-229
EPI-230
EPI-235
EPI-236
EPI-242
EPI-243
EPI-246
EPI-247

Sample list 20160906

EPI-206
EPI-208
EPI-209
EPI-214
EPI-215
EPI-220
EPI-221

Sample list 20160907

EPI-185
EPI-187
EPI-188
EPI-193
EPI-194
EPI-199
EPI-200
EPI-205

Sample list 20160908

EPI-167
EPI-168
EPI-169
EPI-170
EPI-175
EPI-176
EPI-181
EPI-182
EPI-184

Sample list 20160909

EPI-119
EPI-120
EPI-127
EPI-128
EPI-135
EPI-136
EPI-143
EPI-145
EPI-151
EPI-152
EPI-153
EPI-154
EPI-159
EPI-160
EPI-161
EPI-162

Sample list 20160912

Homogenization method was changed to crushing with metal pestle in plastic tube to minimize loss of tissue homogenate on the side of the mortar due to the small size of the samples

EPI-41
EPI-42
EPI-43
EPI-44
EPI-45
EPI-46
EPI-47
EPI-48
EPI-49
EPI-50
EPI-51
EPI-52
EPI-53
EPI-54
EPI-55
EPI-56
EPI-103
EPI-104
EPI-111
EPI-113
EPI-309-Siphon The tip of siphon was cut off and homogenized so that I can test the RNA extraction in the absence of gut content.
EPI-309-Body The remainder was homogenized and put in a different tube to give a mix of siphon and body tissues.

Conclusions

All samples for initial library prep are homogenized.
There should be more then enough tissue in each tube for multiple RNA or DNA extractions, with the exception of the earliest stage samples.
I will test RNA quality from a -80 stored sample See sample list
I will test RNA quality from the siphon only sample (309 siphon above) and the siphon plus body sample (309 body)
Tests of different samples will identify if noisy peaks in prior extractions are due to gut contents or degradation.

Written on September 12, 2016