Grace’s Notebook: Crab RNA extractions with Qubit results

Today I ran 2ul of the 24 samples I extracted yesterday. 20 out of 24 had RNA. Details in post.

Prep

Labeled tubes

• 24 RNase-free snap cap tubes (for preparing the 35ul sample)
• 24 RNase-free snap cap tubes (with C. bairdi RNA, tube number, and date)
• 24 yellow zymo spin column lids (Next time also label collection tube)
• 24 clear zymo spin column lids

Grabbed 100% ethanol in a 15ml tube, and RNase-free water in a 15ml tube.

P1000, P200, P20 and tips

Sample prep

Tubes I grabbed:

status	tube number
infected	15
infected	133
infected	144
infected	81
infected	101
infected	27
infected	163
infected	109
infected	103
infected	62
infected	8
infected	19
uninfected	91
uninfected	10
uninfected	119
uninfected	32
uninfected	53
uninfected	48
uninfected	34
uninfected	121
uninfected	108
uninfected	111
uninfected	50
uninfected	41

1. Let pelleted hemolymph thaw, then vortexed for a second.
2. Transfered 35ul of the slurry to a labeled snap cap tube (some tubes (27, 62, 19) only contained ~35ul, whereas other tubes still had a lot left).
3. Added 35ul of RNase free water
4. Added 280 ul Lysis buffer
5. Mixed all 350ul of liquid by vortexing.

Purification

1. Transfered 350ul of sample into yellow spin column.
2. Spun 10,000 g 30s.
3. Saved DNA on the column for later.
4. Saved flowthrough with RNA and continued
5. Added 350ul 100% ethanol and pipet to mix.
6. Transfer all 700ul to clear spin column.
7. Spun 10,000 g 30 s. Discard flow-through

At the end of Step 7, there was white crystal-y stuff in tubes 144, 8.

1. Added 400ul DNA/RNA prep buffer. Spun 10,000g 30 s

At end of Step 8, tubes 15, 10, 53, 121 still had some liquid on the column

1. Add 700 ul DNA/RNA wash buffer. Spin 10,000 g 30s

At end of step 9, 163, 10, 121, still had liquid on column. Spun these again at 10,000 g 30 s. Then they were fine.

1. Added 400 ul DNA/RNA wash buffer. Spin 10,000 g 2 minutes. Transfered column to fully labeled RNase-free snap caps.
2. Added 15ul RNase-free water to column matrix and let sit for 5 minutes. Spun to elute 10,000 g 2 minutes.

Put samples in -80C over night becuase I left.

Qubit

Ran 2ul of each sample on Qubit.

20/24 samples had RNA.

Link to data

Extracted RNA is in -80, Rack 7, col 3, row 4

(Need to move hemolymph pellets back to their respectve boxes still. Currently hemolymph pellets from this extraction are in the -80 in the same box as the pelleted RNA.)

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Sam’s Notebook: FastQC-MultiQC – C.bairdi RNAseq Day 12 26 Infected Uninfected

After receiving the rest of the crab data and concatenating it all together, I ran FastQC and MultiQC on the FastQ files.

Sam’s Notebook: Data Received – C.bairdi RNAseq Day9-12-26 Infected-Uninfected

Previously, we “received” this data, but it turns out it was incomplete (see 20191003).

Today, we finally received all the RNAseq data (>50M reads per samples) back from NWGC that we submitted on 20190521!

The second round of data is in addition to the data we received on 20191003. So, to simplify some of the data management and downstream processing of these files, I decided to concatenate the two sets of file. Concatenation is documented in this Jupyter Notebook (GitHub):

• 20191024_swoose_cbai_fastq_concatenation.ipynb

Here’s a table with the library names and the FastQ naming schemes.

NWGC Sample ID	Investigator Sample ID
329772	D9_infected
329773	D9_uninfected
329774	D12_infected
329775	D12_uninfected
329776	D26_infected
329777	D26_uninfected

The two samples with strikeouts above failed sequencing. See the previous post from 20191003 about data delivery for all the info on those two samples.