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Supplementary Information Optimization of a Method For Supplementary Information Optimization of a method for the simultaneous extraction of polar and non-polar oxylipin metabolites, DNA, RNA, small RNA, and protein from a single small tissue sample Yu Hasegawa, Yurika Otoki, Shannon McClorry, Laurynne C. Coates, Rachel L. Lombardi, Ameer Y. Taha, Carolyn M. Slupsky Procedure for Methods A and B For Methods A and B, the following steps were modified: 3.1. Preparation of Reagents 1. Prepare chloroform:methanol (2:1) with 0.002% BHT [Solution 1]. Pre-chill in a -20 °C freezer. 2. Prepare 1 mM EDTA dissolved in Type I water [Solution 2]. Pre-chill to 4 °C. 3. Prepare chloroform:methanol (10:1) [Solution 3]. Pre-chill in a -20 °C freezer. 3.3. Metabolite Extraction 3.3.1. Method A 1. Add 1600 µL of chloroform, 800 µL of methanol, and 600 µL of Type I ultrapure water to tubes with ground brain tissue and mix by vortexing for 20 seconds. 2. Centrifuge the tubes for 15 min at 2,000 rpm at 0 °C to separate the sample into three layers. 3. Collect the upper layer into a new 15 mL conical centrifuge tube. Do not disturb the cell layer. Keep the tube on ice and proceed to step 22. 4. Using a 9-inch glass Pasteur pipette, collect the bottom layer and place in a new 8 mL glass tube. Place the tube on ice and proceed to step 31. 5. Proceed to step 42 to process the middle layer. 3.3.2. Method B 1. Add 2.4 mL of cold Solution 1 into the 8 mL glass tube with the cryoground tissue. 2. Add 600 µL of Solution 2. 3. Cap carefully and Vortex for 20 s at max speed, and centrifuge for 15 min at 2,000 rpm at 0 °C. 4. Using a 9-inch glass Pasteur pipette, collect the bottom layer and place in a new 8 mL glass tube. Place the tube on ice. 5. Add 1.4 mL of cold Solution 3 to the remaining upper and cell layer. 6. Vortex for 10 s at max speed, and centrifuge for 15 min at 2,000 rpm at 0 °C. 7. Collect the upper layer into a new 15 mL conical centrifuge tube. Do not disturb the cell layer. Keep the tube on ice and proceed to step 22. 8. Collect the bottom layer with a Pasteur pipette, and add to the glass tube from step 4. Place the tube on ice and proceed to step 31. 9. Proceed to step 42 to process the middle layer. Supplementary Tables Table S1. Gradient conditions for oxylipin separation via LC-MS/MS analysis. SolVent B consisted of acetonitrile:methanol (80:15) containing 0.1% acetic acid. Time Solvent B Flow (min) concentration (%) (min/mL) 0 35 0.3 3 40 0.25 4 48 0.25 10 60 0.25 20 70 0.25 24 85 0.25 24.5 85 0.25 24.6 100 0.35 26 100 0.35 26.1 35 0.35 27.3 35 0.3 28 Stop Table S2. Optimized mass-spectrometry parameters for measuring oxylipins. Cell Precursor Product Frag CE Rt Compound name Acc Internal standard Ion (m/z) Ion (m/z) (V) (V) (min) (V) 20-COOH-LTB4 365.2 347.2 120 7 4 4.0 d4-LTB4 ResolVin E1 349.3 195 115 10 4 4.6 d4-PGE2 d4-6-keto-PGF1a 373.3 167.1 90 19 4 4.7 - 6-keto-PGF1a 369.3 163.2 90 22 4 4.7 d4-6-keto-PGF1a 20-OH-LTB4 351.2 195.2 95 13 4 5.0 d4-LTB4 d4-TXB2 373.3 173.2 105 10 4 6.1 - TXB2 369.2 169.1 80 10 4 6.1 d4-TXB2 PGE3 349.3 269.2 120 7 4 6.2 d4-PGE2 PGD3 349.3 269.2 120 7 4 6.5 d4-PGE2 9,12,13-TriHOME 329.2 211.1 125 16 4 6.6 d4-PGE2 9,10,13-TriHOME 329.2 171.1 110 16 4 6.7 d4-PGE2 PGF2a 353.2 309.2 120 10 4 6.7 d4-PGE2 d4-PGE2 355.2 275.3 90 7 4 7.0 - PGE2 351.2 271.3 80 10 4 7.0 d4-PGE2 PGD1 353.3 317.2 75 7 4 7.2 d4-PGE2 PGE1 353.3 317.2 75 7 4 7.3 d4-PGE2 PGD2 351.2 271.3 80 10 4 7.3 d4-PGE2 LTD4 495.3 177.1 55 13 4 7.8 d4-LTB4 LXA4 351.2 115.2 95 10 4 8.1 d4-LTB4 LTC4 624.3 272.1 70 22 4 9.6 d4-LTB4 LTE4 438.2 333.3 90 13 4 9.7 d4-LTB4 PGJ2 333.3 189.2 90 10 4 9.9 d4-PGE2 PGB2 333.3 175.1 125 13 4 10.0 d4-PGE2 6-trans-LTB4 335.2 195.1 125 7 4 10.8 d4-LTB4 5,15-DiHETE 335.2 173.2 95 7 4 10.8 d11-14,15-DiHETrE 5,6-DiHETE 335.2 115.2 90 4 4 10.9 d11-14,15-DiHETrE 8,15-DiHETE 335.2 235.2 90 7 4 11.1 d11-14,15-DiHETrE 17,18-DiHETE 335.3 247.2 105 7 4 11.7 d11-14,15-DiHETrE d4-LTB4 339.2 197.2 80 10 4 11.9 - LTB4 335.2 195.1 125 7 4 11.9 d4-LTB4 14,15-DiHETE 335.3 207.2 95 7 4 12.3 d11-14,15-DiHETrE 9,10-DiHOME 313.2 201.2 130 16 4 12.42 d11-14,15-DiHETrE 12,13-DiHOME 313.2 183.2 130 16 4 12.7 d11-14,15-DiHETrE 14,15-DiHETrE 337.2 207.1 130 10 4 13.8 d11-14,15-DiHETrE d11-14,15- 348.2 207.1 125 10 6 13.8 - DiHETrE LTB3 337.2 195.2 120 7 4 14.2 d4-LTB4 11,12-DiHETrE 337.2 167.1 120 13 4 14.8 d11-14,15-DiHETrE 9-HOTrE 293.2 171.2 110 4 4 15.3 d4-9HODE 8,9-DiHETrE 337.2 127.1 85 13 4 15.6 d11-14,15-DiHETrE 13-HOTrE 293.2 195.1 125 10 4 15.6 d4-9HODE 15-deoxy-PGJ2 315.2 271.2 130 4 4 16.1 d4-PGE2 d6-20-HETE 325.2 281.2 110 7 4 16.5 - 20-HETE 319.2 275.1 125 10 4 16.5 d6-20-HETE 15-HEPE 317.2 219.2 90 4 4 16.6 d8-5-HETE 5,6-DiHETrE 337.2 145.1 85 7 4 16.7 d11-14,15-DiHETrE 8-HEPE 317.2 155.2 115 7 4 17.0 d8-5-HETE 12-HEPE 317.2 179.2 110 4 4 17.2 d8-5-HETE 5-HEPE 317.2 115.1 115 4 4 17.8 d8-5-HETE d4-9HODE 299.2 172.3 90 13 4 18.0 - 13-HODE 295.2 195.2 95 13 4 18.0 d4-9HODE 9-HODE 295.2 171.1 120 10 4 18.0 d4-9HODE 15-HETE 319.2 219.2 120 4 4 19.1 d8-5-HETE 17(18)-EpETE 317.2 215.2 130 4 4 19.2 d-11-11(12)EpEtrE 13-oxo-ODE 293.2 195.1 95 13 4 19.3 d6-20-HETE 17-HDoHE 343.2 281.2 95 4 4 19.5 d4-9HODE 11-HETE 319.2 167.2 100 7 4 19.5 d8-5-HETE 9-HETE 319.2 167.2 80 7 4 19.8 d8-5-HETE 9-oxo-ODE 293.2 185.1 90 13 4 20.0 d6-20-HETE 15-oxo-ETE 317.2 113.1 125 10 6 20.1 d8-5-HETE 14(15)-EpETE 317.2 207.2 100 4 4 20.2 d-11-11(12)EpEtrE 8-HETE 319.2 155.2 120 7 4 20.4 d8-5-HETE 11(12)-EpETE 317.2 167.2 90 4 4 20.5 d-11-11(12)EpEtrE 12-HETE 319.2 179.2 120 7 4 20.5 d8-5-HETE 8(9)-EpETE 317.2 127.2 115 4 4 20.8 d-11-11(12)EpEtrE 12-oxo-ETE 317.2 153.1 115 7 4 21.1 d8-5-HETE 15(S)-HETrE 321.2 221.2 85 7 4 21.1 d8-5-HETE 5-HETE 319.2 115.1 90 10 4 21.2 d8-5-HETE d8-5-HETE 327.2 116.1 75 7 4 21.2 - 12(13)EpOME 295.3 195.2 95 7 4 22.5 d-11-11(12)EpEtrE 19(20)-EpDPE 343.2 241.2 130 7 4 22.5 d-11-11(12)EpEtrE 14(15)-EpETrE 319.2 219.3 130 4 4 22.8 d-11-11(12)EpEtrE 9(10)-EpOME 295.3 171.1 100 7 4 22.8 d-11-11(12)EpEtrE 16(17)-EpDPE 343.2 233.2 130 4 4 23.3 d-11-11(12)EpEtrE 13(14)-EpDPE 343.2 193.2 80 4 4 23.4 d-11-11(12)EpEtrE 5-oxo-ETE 317.2 273.2 120 7 4 23.4 d8-5-HETE 11(12)-EpETrE 319.2 167.2 105 4 4 23.5 d-11-11(12)EpEtrE d-11-11(12)EpEtrE 330.2 167.2 80 7 4 23.5 - 10(11)-EpDPE 343.2 153.2 90 4 4 23.6 d-11-11(12)EpEtrE 7(8)-EpDPE 343.2 113.1 85 4 4 23.8 d-11-11(12)EpEtrE 8(9)-EpETrE 319.2 167.2 90 4 4 23.9 d-11-11(12)EpEtrE 5(6)-EpETrE 319.2 191.1 115 4 4 24.2 d-11-11(12)EpEtrE Abbr: m/z, mass to charge ratio; CE, collision energy; Rt, Retention Time.
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