DNA/RNA extractions from E5 project

Re-Extractions from Acropora from the first timepoint

---

Extraction Date: September 29, 2022

Samples

Tube number	Timepoint	Species	Colony ID	Coll date	Site
31	January	Acropora	ACR-267	20200103	2
33	January	Acropora	ACR-265	20200103	2
35	January	Acropora	ACR-234	20200103	2
39	January	Acropora	ACR-244	20200103	2
41	January	Acropora	ACR-225	20200103	2
45	January	Acropora	ACR-256	20200103	2
47	January	Acropora	ACR-228	20200103	2
49	January	Acropora	ACR-237	20200103	2
55	January	Acropora	ACR-229	20200103	2

Extraction notes

• For each sample I took 300ul the RNA/DNA shield and added it to a new 1.5ml tube containing 15ul of ProK, and 30ul of ProK digestion buffer
• Samples sat for 15 minutes at room temperate
• Spun down samples for 3 minutes at 9000 rcf and then transfer the supernatant to new tube without disturbing the pellet
• All subsequent spins were done for 1 minute or 2.30 minutes
• Did two washes with 700ul of wash buffer for both the DNA and RNA
• Then followed the protocol as described in protocol

Qubit

• Used Broad range dsDNA and RNA Qubit Protocol
• All samples read twice, standard only read once

DNA

Tube number	RFU	DNA 1 (ng/uL)	DNA 2 (ng/uL)	Average
Standard 1	208.46
Standard 2	24328.01
31		16.8	16.4	16.6
33		11.2	11.0	11.1
35		7.46	4.22	5.84
39		ND	ND	ND
41		2.02	ND	2.0
45		21.2	20.6	20.9
47		22.2	20.6	21.4
49		8.78	9.1	8.94
55		15.1	14.9	15.0

RNA

Tube number	RFU	RNA 1 (ng/uL)	RNA 2 (ng/uL)	Average
Standard 1	197.77
Standard 2	21529.84
31		17.0	17.0	17.0
33		11.4	11.2	11.3
35		ND	ND	ND
39		11.0	11.2	11.1
41		16.0	16.0	16.0
45		15.6	15.6	15.6
47		18.6	18.6	18.6
49		13.6	13.2	13.4
55		10.6	10.4	10.5

Tape Station

• Samples not analyzed

Gel

• Modified from this protocol
• Added 0.75g of agarose and 50ml of 1x TAE to flask and microwaved for 45 seconds. This makes a 1.5% gel
• Once cool enough to touch added 2ul of gel green stain
• Swirled and poured into gel mould with comb
• Once solidified, covered with 1X TAE as a running buffer
• Added 1ul of purple loading dye to each of my QC strip tube samples. I had ~9ul of DNA leftover from QC and ~8ul of RNA
• Loaded my gel with the DNA first, then skipped a well and then the RNA
• Ran the gel for 60 minutes at 60 volts

Addtional Notes

• #35 doesn’t look great, the rest look good though!