Metabolite and lipid sample prep
e5 sample prep for lipid and metabolite analysis
To characterize lipids and metabolites in the e5 timeseries data, we have to homogenize and separate the samples before sending them to the UW facility. We first sent them 4 test samples to see if these samples would work. The lipids worked great but the metabolite data was lacking some key metabolites – we may not have given them enough sample as input and the instruments may have gotten disrupted by salt since we used 10x PBS to airbrush the samples. See the former protocol e5 timeseries molecular github for information about test samples.
To remedy these issues, Ariana and I developed the following protocol, which I followed for all samples unless otherwise noted.
The major changes of the protocol:
- Use LCMS grade water for airbrushing
- Airbrush fragment primarily with air and remove any residual tissue with water + airbrush, which should lead to a more concentrated sample
- Collect homogenate from each sample for protein assay
- Run protein assay to quantify the ug/mL of protein in tissue
Sample prep
Below are the details for the samples I prepped. There are 96 samples total. I will continue to add to this table as I complete each sample.
| Sample | Timepoint | Sample Name | Species | Site | Frozen Frag | Fragment bag (M1 or M2) | Bag notes | Jill finding note | Date of airbrushing | Airbrush notes | Serial number | Metabolite volume (uL) | Lipid volume (uL) | Backup volume (uL) | Protein volume (uL) | Total volume (mL) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| POR-73 | TP1 | POR-73_TP1 | Porites evermanni | Manava (site 1) | yes | orange | From “undated” January bag - Zoe has picture | 20241126 | 1 | 1000 | 1000 | 1000 | 1000 | 6 | ||
| POC-42 | TP3 | POC-42_TP3 | Pocillopora tuahiniensis | Manava (site 1) | yes | pink | 20241126 | 2 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| ACR-145 | TP4 | ACR-145_TP4 | Acropora pulchra | Manava (site 1) | yes | grey | 20241126 | 3 | 1000 | 1000 | 1000 | 1000 | 5.5 | |||
| POC-53 | TP3 | POC-53_TP3 | Pocillopora tuahiniensis | Manava (site 1) | yes | grey | 20241126 | 4 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POC-52 | TP1 | POC-52_TP1 | Pocillopora tuahiniensis | Manava (site 1) | yes | orange | From “undated” January bag - Zoe has picture | 20241126 | 5 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| POC-259 | TP4 | POC-259_TP4 | Pocillopora tuahiniensis | Mahana (site 2) | yes | pink | 20241126 | 6 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| POC-42 | TP4 | POC-42_TP4 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | 20241126 | 7 | 1000 | 1000 | 1000 | 1000 | 9 | |||
| POC-53 | TP1 | POC-53_TP1 | Pocillopora tuahiniensis | Manava (site 1) | yes | orange | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20241126 | 8 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| POR-216 | TP1 | POR-216_TP1 | Porites evermanni | Mahana (site 2) | yes | green | 20241126 | 9 | 1000 | 1000 | 1000 | 1000 | 9 | |||
| POR-72 | TP3 | POR-72_TP3 | Porites evermanni | Manava (site 1) | yes | grey | 20241126 | 10 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| ACR-237 | TP3 | ACR-237_TP3 | Acropora pulchra | Mahana (site 2) | yes | green | 20241126 | 11 | 1000 | 1000 | 1000 | 500 | 3.5 | |||
| POR-216 | TP3 | POR-216_TP3 | Porites evermanni | Mahana (site 2) | yes | green | 20241126 | 12 | 1000 | 1000 | 1000 | 500 | 3.5 | |||
| POC-201 | TP3 | POC-201_TP3 | Pocillopora tuahiniensis | Mahana (site 2) | yes | grey | 20241201 | 13 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| POR-216 | TP4 | POR-216_TP4 | Porites evermanni | Mahana (site 2) | yes | pink | found 2 | 20241201 | 14 | 1000 | 1000 | 1000 | 1000 | 5.5 | ||
| POR-262 | TP3 | POR-262_TP3 | Porites evermanni | Mahana (site 2) | yes | green | 20241201 | 15 | 1000 | 1000 | 1000 | 1000 | 11 | |||
| ACR-186 | TP3 | ACR-186_TP3 | Acropora pulchra | Manava (site 1) | yes | pink | 20241201 | 16 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| ACR-186 | TP1 | ACR-186_TP1 | Acropora pulchra | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20241201 | 17 | 500 | 500 | 500 | 500 | 2 | ||
| ACR-244 | TP4 | ACR-244_TP4 | Acropora pulchra | Mahana (site 2) | yes | pink | 20241201 | 18 | 1000 | 1000 | 1000 | 500 | 3.5 | |||
| POR-72 | TP2 | POR-72_TP2 | Porites evermanni | Manava (site 1) | yes | yellow | From “undated” March bag - Zoe has picture | 20241202 | 19 | 1000 | 1000 | 1000 | 1000 | 5.5 | ||
| ACR-229 | TP1 | ACR-229_TP1 | Acropora pulchra | Mahana (site 2) | yes | red | Whirlpak label is “5”, but this code has been confirmed by notebook. Zoe has picture. | 20241202 | 20 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| POC-57 | TP4 | POC-57_TP4 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | found 2 | 20241202 | 21 | 1000 | 1000 | 1000 | 1000 | 8 | ||
| POC-259 | TP1 | POC-259_TP1 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20241202 | 22 | 1000 | 1000 | 500 | 500 | 3 | |||
| POC-255 | TP3 | POC-255_TP3 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20241202 | 23 | 1000 | 1000 | 1000 | 1000 | 11 | |||
| POR-69 | TP4 | POR-69_TP4 | Porites evermanni | Manava (site 1) | yes | blue | 20241202 | 24 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POC-57 | TP1 | POC-57_TP1 | Pocillopora tuahiniensis | Manava (site 1) | yes | orange | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20241202 | 25 | 1000 | 1000 | 1000 | 1000 | 7.5 | ||
| ACR-229 | TP4 | ACR-229_TP4 | Acropora pulchra | Mahana (site 2) | yes | pink | found 2 | 20241202 | 26 | 1000 | 1000 | 1000 | 1000 | 5 | ||
| POR-260 | TP2 | POR-260_TP2 | Porites evermanni | Mahana (site 2) | yes | green | Check handwriting - We believe this is March - no date. Zoe has picture | 20241202 | 27 | 1000 | 1000 | 250 | 250 | 2.5 | ||
| ACR-145 | TP1 | ACR-145_TP1 | Acropora pulchra | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | found 2 | 20241202 | 28 | 1000 | 1000 | 1000 | 1000 | 5 | |
| POR-69 | TP2 | POR-69_TP2 | Porites evermanni | Manava (site 1) | yes | green | No date on whirlpak, but from March - based on handwriting. Zoe has picture, | 20241202 | 29 | 1000 | 1000 | 1000 | 1000 | 4.5 | ||
| ACR-265 | TP3 | ACR-265_TP3 | Acropora pulchra | Mahana (site 2) | yes | green | 20241202 | 30 | 1000 | 1000 | 500 | 500 | 3 | |||
| POR-262 | TP2 | POR-262_TP2 | Porites evermanni | Mahana (site 2) | yes | yellow | 20241204 | 31 | 500 | 500 | 500 | 500 | 2 | |||
| POR-74 | TP4 | POR-74_TP4 | Porites evermanni | Manava (site 1) | yes | blue | 20241204 | 32 | 1000 | 1000 | 1000 | 1000 | 5.5 | |||
| POR-262 | TP1 | POR-262_TP1 | Porites evermanni | Mahana (site 2) | yes | green | found 2 | 20241204 | 33 | 1000 | 1000 | 1000 | 1000 | 6 | ||
| POC-201 | TP1 | POC-201_TP1 | Pocillopora tuahiniensis | Mahana (site 2) | yes | red | 20241204 | 34 | 1000 | 1000 | 1000 | 1000 | 4.5 | |||
| POR-69 | TP3 | POR-69_TP3 | Porites evermanni | Manava (site 1) | yes | pink | 20241204 | 35 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| ACR-229 | TP3 | ACR-229_TP3 | Acropora pulchra | Mahana (site 2) | yes | green | 20241204 | 36 | 1000 | 1000 | 500 | 500 | 3 | |||
| ACR-173 | TP3 | ACR-173_TP3 | Acropora pulchra | Manava (site 1) | yes | pink | 20241204 | 37 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POC-53 | TP4 | POC-53_TP4 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | 20241204 | 38 | 1000 | 1000 | 1000 | 1000 | 5.5 | |||
| POR-216 | TP2 | POR-216_TP2 | Porites evermanni | Mahana (site 2) | yes | green | No date on whirlpak, but from March - based on handwriting. Zoe has picture, | 20241204 | 39 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| POR-73 | TP4 | POR-73_TP4 | Porites evermanni | Manava (site 1) | yes | blue | found 2 | 20241204 | 40 | 1000 | 1000 | 1000 | 1000 | 8 | ||
| POR-69 | TP1 | POR-69_TP1 | Porites evermanni | Manava (site 1) | yes | orange | From “undated” January bag - Zoe has picture | 20241204 | 41 | 1000 | 1000 | 1000 | 1000 | 4.5 | ||
| POR-74 | TP2 | POR-74_TP2 | Porites evermanni | Manava (site 1) | yes | green | No date on whirlpak, but from March - based on handwriting. Zoe has picture, | 20241204 | 42 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| POC-219 | TP3 | POC-219_TP3 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20241205 | 43 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| POR-245 | TP1 | POR-245_TP1 | Porites evermanni | Mahana (site 2) | yes | green | 20241205 | 44 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| POR-236 | TP1 | POR-236_TP1 | Porites evermanni | Mahana (site 2) | yes | green | 20241205 | 45 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POR-74 | TP3 | POR-74_TP3 | Porites evermanni | Manava (site 1) | yes | pink | 20241205 | 46 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| ACR-139 | TP3 | ACR-139_TP3 | Acropora pulchra | Manava (site 1) | yes | pink | 20241205 | 47 | 1000 | 1000 | 1000 | 1000 | 4.5 | |||
| ACR-237 | TP1 | ACR-237_TP1 | Acropora pulchra | Mahana (site 2) | yes | orange | Whirlpak label is “2”, but this code has been confirmed by notebook. Zoe has picture. | 20241205 | 48 | 1000 | 1000 | 500 | 500 | 3 | ||
| ACR-244 | TP1 | ACR-244_TP1 | Acropora pulchra | Mahana (site 2) | yes | red | Whirlpak label is “14”, but this code has been confirmed by notebook. Zoe has picture. | 20250115 | 49 | 1000 | 1000 | 500 | 500 | 3 | ||
| ACR-139 | TP1 | ACR-139_TP1 | Acropora pulchra | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20250115 | 50 | 1000 | 1000 | 1000 | 1000 | 4.5 | ||
| POC-40 | TP3 | POC-40_TP3 | Pocillopora tuahiniensis | Manava (site 1) | yes | pink | 20250115 | 51 | 1000 | 1000 | 1000 | 1000 | 6 | |||
| POC-222 | TP1 | POC-222_TP1 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20250115 | 52 | 1000 | 1000 | 1000 | 1000 | 6 | |||
| POC-255 | TP4 | POC-255_TP4 | Pocillopora tuahiniensis | Mahana (site 2) | yes | pink | 20250115 | 53 | 1000 | 1000 | 1000 | 1000 | 5.5 | |||
| ACR-237 | TP4 | ACR-237_TP4 | Acropora pulchra | Mahana (site 2) | yes | pink | 20250115 | Bag leaked while airbrushing | 54 | 1000 | 1000 | 500 | 500 | 3 | ||
| POR-72 | TP4 | POR-72_TP4 | Porites evermanni | Manava (site 1) | yes | blue | 20250117 | 55 | 1000 | 1000 | 1000 | 1000 | 7 | |||
| POC-57 | TP3 | POC-57_TP3 | Pocillopora tuahiniensis | Manava (site 1) | yes | pink | 20250117 | 56 | 1000 | 1000 | 1000 | 1000 | 6 | |||
| POC-40 | TP4 | POC-40_TP4 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | 20250117 | 57 | 1000 | 1000 | 1000 | 1000 | 12 | |||
| ACR-150 | TP3 | ACR-150_TP3 | Acropora pulchra | Manava (site 1) | yes | pink | 20250117 | 58 | 1000 | 1000 | 500 | 500 | 3 | |||
| POR-74 | TP1 | POR-74_TP1 | Porites evermanni | Manava (site 1) | yes | blue | 20250117 | Bag leaked while airbrushing | 59 | 1000 | 1000 | 500 | 500 | 3 | ||
| POC-222 | TP4 | POC-222_TP4 | Pocillopora tuahiniensis | Mahana (site 2) | yes | pink | found 2 | 20250117 | 60 | 1000 | 1000 | 500 | 500 | 3 | ||
| POC-255 | TP1 | POC-255_TP1 | Pocillopora tuahiniensis | Mahana (site 2) | yes | red | 20250117 | 61 | 1000 | 1000 | 1000 | 1000 | 12 | |||
| POR-245 | TP2 | POR-245_TP2 | Porites evermanni | Mahana (site 2) | yes | yellow | From “undated” March bag - Zoe has picture | 20250117 | 62 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| ACR-225 | TP1 | ACR-225_TP1 | Acropora pulchra | Mahana (site 2) | yes | orange | Whirlpak label is “6”, but this code has been confirmed by notebook. Zoe has picture. | 20250117 | 63 | 1000 | 1000 | 1000 | 1000 | 7.5 | ||
| POR-73 | TP3 | POR-73_TP3 | Porites evermanni | Manava (site 1) | yes | grey | 20250117 | 64 | 1000 | 1000 | 1000 | 1000 | 7 | |||
| ACR-225 | TP4 | ACR-225_TP4 | Acropora pulchra | Mahana (site 2) | yes | pink | 20250117 | 65 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| ACR-139 | TP4 | ACR-139_TP4 | Acropora pulchra | Manava (site 1) | yes | blue | 20250117 | 66 | 1000 | 1000 | 500 | 500 | 3 | |||
| ACR-150 | TP1 | ACR-150_TP1 | Acropora pulchra | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20250117 | Very small piece (1-2cm) | 67 | 500 | 500 | 500 | 500 | 2 | |
| POR-260 | TP3 | POR-260_TP3 | Porites evermanni | Mahana (site 2) | yes | green | 20250117 | 68 | 1000 | 1000 | 1000 | 1000 | 6 | |||
| POR-236 | TP2 | POR-236_TP2 | Porites evermanni | Mahana (site 2) | yes | green | No date on whirlpak, but from March - based on handwriting. Zoe has picture, | 20250117 | 69 | 1000 | 1000 | 1000 | 1000 | 7 | ||
| POC-222 | TP3 | POC-222_TP3 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20250117 | 70 | 1000 | 1000 | 1000 | 1000 | 6 | |||
| ACR-173 | TP1 | ACR-173_TP1 | Acropora pulchra | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20250117 | 71 | 1000 | 1000 | 1000 | 1000 | 7 | ||
| POC-42 | TP1 | POC-42_TP1 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20250117 | 72 | 1000 | 1000 | 1000 | 1000 | 7 | ||
| POR-83 | TP4 | POR-83_TP4 | Porites evermanni | Manava (site 1) | yes | blue | 20250118 | 73 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POC-40 | TP1 | POC-40_TP1 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | No date on whirlpak, but from January - based on handwriting. Zoe has picture, | 20250118 | 74 | 1000 | 1000 | 1000 | 1000 | 5 | ||
| POR-73 | TP2 | POR-73_TP2 | Porites evermanni | Manava (site 1) | yes | green | No date on whirlpak, but from March - based on handwriting. Zoe has picture, | 20250118 | 75 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| ACR-145 | TP3 | ACR-145_TP3 | Acropora pulchra | Manava (site 1) | yes | pink | 20250118 | Very small piece (1-2cm) | 76 | 1000 | 1000 | 500 | 500 | 3 | ||
| POR-262 | TP4 | POR-262_TP4 | Porites evermanni | Mahana (site 2) | yes | pink | 20250118 | 77 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| POC-52 | TP4 | POC-52_TP4 | Pocillopora tuahiniensis | Manava (site 1) | yes | blue | 20250118 | Bag leaked while airbrushing | 78 | 1000 | 1000 | 1000 | 1000 | 11 | ||
| POC-219 | TP1 | POC-219_TP1 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20250118 | 79 | 1000 | 1000 | 1000 | 1000 | 12 | |||
| POR-83 | TP2 | POR-83_TP2 | Porites evermanni | Manava (site 1) | yes | yellow | From “undated” March bag - Zoe has picture | 20250118 | Bag leaked while airbrushing | 80 | 1000 | 1000 | 1000 | 1000 | 8 | |
| ACR-173 | TP4 | ACR-173_TP4 | Acropora pulchra | Manava (site 1) | yes | blue | 20250118 | 81 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| ACR-150 | TP4 | ACR-150_TP4 | Acropora pulchra | Manava (site 1) | yes | blue | 20250118 | 82 | 1000 | 1000 | 1000 | 1000 | 10 | |||
| POR-245 | TP3 | POR-245_TP3 | Porites evermanni | Mahana (site 2) | yes | grey | 20250118 | 83 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POC-52 | TP3 | POC-52_TP3 | Pocillopora tuahiniensis | Manava (site 1) | yes | pink | 20250118 | 84 | 1000 | 1000 | 1000 | 1000 | 6 | |||
| ACR-244 | TP3 | ACR-244_TP3 | Acropora pulchra | Mahana (site 2) | yes | green | 20250119 | Very small piece (1-2cm) | 85 | 1000 | 1000 | 1000 | 1000 | 4 | ||
| POR-260 | TP4 | POR-260_TP4 | Porites evermanni | Mahana (site 2) | yes | pink | 20250119 | 86 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POR-83 | TP3 | POR-83_TP3 | Porites evermanni | Manava (site 1) | yes | pink | 20250119 | 87 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| ACR-186 | TP4 | ACR-186_TP4 | Acropora pulchra | Manava (site 1) | yes | blue | 20250119 | 88 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| ACR-225 | TP3 | ACR-225_TP3 | Acropora pulchra | Mahana (site 2) | yes | green | 20250119 | 89 | 1000 | 1000 | 1000 | 1000 | 4 | |||
| POC-259 | TP3 | POC-259_TP3 | Pocillopora tuahiniensis | Mahana (site 2) | yes | green | 20250119 | 90 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| ACR-265 | TP1 | ACR-265_TP1 | Acropora pulchra | Mahana (site 2) | yes | green | Whirlpak label is “11”, but this code has been confirmed by notebook. Zoe has picture. | 20250119 | 91 | 1000 | 1000 | 1000 | 1000 | 5 | ||
| POC-219 | TP4 | POC-219_TP4 | Pocillopora tuahiniensis | Mahana (site 2) | yes | pink | 20250119 | 92 | 1000 | 1000 | 1000 | 1000 | 5 | |||
| POR-260 | TP1 | POR-260_TP1 | Porites evermanni | Mahana (site 2) | yes | green | 20250119 | 93 | 1000 | 1000 | 1000 | 1000 | 14 | |||
| POR-245 | TP4 | POR-245_TP4 | Porites evermanni | Mahana (site 2) | yes | pink | label says “298(OG 245)” | 20250119 | 94 | 1000 | 1000 | 500 | 500 | 3 | ||
| POR-72 | TP1 | POR-72_TP1 | Porites evermanni | Manava (site 1) | yes | red | No date on whirlpak but from “dated” January bag - Zoe has picture | 20250119 | 95 | 1000 | 1000 | 1000 | 1000 | 5 | ||
| POR-83 | TP1 | POR-83_TP1 | Porites evermanni | Manava (site 1) | yes | orange | From “undated” January bag - Zoe has picture | 20250119 | 96 | 1000 | 1000 | 1000 | 1000 | 7 |
In the table, the serial number is the number on the tube that will be sent to UW for analysis. Sample prep complete on 1/19/25.
Written on November 26, 2024