= 75*4
DB print(DB)
[1] 300
= 5*4
Dnase print(Dnase)
[1] 20
Sarah Tanja
February 8, 2025
December 3, 2024
1C4F, 2C4F, 3C4F = 123C4
1L14F, 2L14F, 3L14F = 123L14
1M4F, 2M4F, 3M4F = 123M4
1H14F, 2H14F, 3H14F = 123H14
Success! I pooled 3 samples together and this yielded enough RNA!
I also tested 3 different lysing protocols, and all worked more or less the same. I skipped the Proteinase K digestion as per the ‘cells’ sample prep instruction in the kit manual. I think I can add this back in if I’m finding protein impurities in the eluted RNA.
date: 13-AUG-2024
kit: Zymo Quick-DNA/RNA Miniprep Plus Kit
Thaw samples to room temp
Vortex to mix
Transfer to Qiagin Tissue Disruption Tube
Homogenize for 1 minute
Centrifuge at 16,000xg for 1 minute to get rid of bubbles
Honogenized for another 1 minute
Split into two aliquots of 700uL & transfer to two new nuclease-free tubes
Twizzled 123L14, 123 M4, and 123H14 for extra mechanical lysing
Added 700uL of DNA/RNA Lysis Buffer to each tube ( a total of 1400uL volume in each tube )
Vortex to mix for 5 seconds
Check to see that embryos have dissolved and liquid is clear
123C4, clear
123L14, clear
123M4, cell debris
123H14, clear
—> Proceed to purification
Sequentially transfer 2800uL of each sample in aliquots of 700uL into yellow Spin-Away Filter in a Collection Tube and centrifuge for 30s at 16,000xg SAVE THE FLOW THROUGH FOR RNA PURIFICATION by tipping flow through into falcon tube
Doubled volume of 100% (200 proof) ethanol to the RNA flow through in a falcon tube and vortexed to mix. End volume of flow through + ethanol = 5mL
Sequentially transfer RNA flow-through + ethanol in volumes =>700uL into the green Zymo Spin IIICG Column in a Collection Tube
Saved 1st 1400uL for protein
This took 7 passes!
Performed DNase I Treatment on green RNA spin column
Warmed Zymo DNase-RNase Free Water to 55C in heat block before elution, and slowly dripped water directly over filter.
eluted DNA volume: 30uL in Zymo DNase-RNase Free Water
eluted RNA volume: 30uL in Zymo DNase-RNase Free Water
sample_id | ng/uL | A260 | A280 | 260/280 | 260/230 |
---|---|---|---|---|---|
123C4 | 43.3 | 1.083 | 0.611 | 1.77 | 1.27 |
123H14 | 7.8 | 0.195 | 0.060 | 3.25 | -0.94 |
123M4 | 90.8 | 2.271 | 1.125 | 2.02 | 1.86 |
123L14 | 16.0 | 0.399 | 0.196 | 2.04 | 1.99 |
123L9 is showing contamination… There is no distinct peak at 260 (like is visible with the other samples).
Using the Invitrogen Thermo Fischer RNA High Sensitivity Assay Kit.
Prepared working solution for 3 samples and two standards:
Qubit RNA HS reagent in DMSO = 1uL * 5 = 6uL
Qubit RNA HS Buffer = 199uL * 5 = 1194uL
standard 1: 91.79
standard 2: calibration error (even after two attempts… I plan to rerun these after getting fresh assay reagents)
RunID: 2024-08-14_043136
sample_id | qubit_rna_1 | qubit_rna_2 |
---|---|---|
123C4 | 47.6 ng/uL | 47.6 ng/uL |
123L14 | 19.6 ng/uL | 19.7 ng/uL |
123M4 | 124 ng/uL | 122 ng/uL |
123H14 | 27.6 ng/uL | 27.6 ng/uL |
RNA samples are stored in -80C ‘Old Friedman’ Sanyo freezer on shelf 1 in coral-embryo-leachate RNA
wax freezer boxes with green label tape:
DNA samples (not quantified) are stored in -20C in JPG Lab FSH 236 in shelf 2 in coral-embryo-leachate DNA
wax freezer box with yellow label tape:
Protein flow-through (not quantified) are stored in -20C in JPG Lab FSH 236 in shelf 2 in coral-embryo-leachate PROTEIN
wax freezer box with blue label tape: