#METABOLOMICS WORKBENCH boryana_ptrva_20230515_132357 DATATRACK_ID:4025 STUDY_ID:ST002707 ANALYSIS_ID:AN004389 PROJECT_ID:PR001678 VERSION 1 CREATED_ON May 19, 2023, 11:32 am #PROJECT PR:PROJECT_TITLE Combining multi-omics and real-time optics to track diurnal transitions in the PR:PROJECT_TITLE choroid plexus and CSF at molecular, spatial, and temporal resolution PR:PROJECT_SUMMARY The choroid plexus (ChP) comprises the blood-CSF barrier and regulates PR:PROJECT_SUMMARY cerebrospinal fluid (CSF) composition. Details of ChP-CSF regulation throughout PR:PROJECT_SUMMARY the day remain unknown, largely due to lack of tools. We developed a platform PR:PROJECT_SUMMARY for analyzing diurnal variations in mouse ChP function. We demonstrate PR:PROJECT_SUMMARY widespread diurnal regulation of ChP secretion and barrier function across hours PR:PROJECT_SUMMARY during the circadian day and in response to feeding cues, resulting in changes PR:PROJECT_SUMMARY in CSF composition. ChP metabolomics uncovered increased dark phase oxidation. PR:PROJECT_SUMMARY Transthyretin (TTR), a thyroid hormone chaperone, exhibited strong diurnal PR:PROJECT_SUMMARY regulation and CSF-TTR levels varied across the day in register with CSF thyroid PR:PROJECT_SUMMARY hormone levels and ChP-TTR expression. Our data will serve as a resource for the PR:PROJECT_SUMMARY community, enabling better understanding of circadian rhythms and ChP diurnal PR:PROJECT_SUMMARY function and regulation. PR:INSTITUTE Boston Childrens Hospital PR:DEPARTMENT Pathology PR:LABORATORY Kanarek Lab PR:LAST_NAME Petrova PR:FIRST_NAME Boryana PR:ADDRESS 300 Longwood Av, Boston, MA, 2115, USA PR:EMAIL boryana.petrova@childrens.harvard.edu PR:PHONE 6173557433 PR:CONTRIBUTORS Boryana Petrova, Ryann Fame #STUDY ST:STUDY_TITLE Levels of T3 (triiodothyronine) and T4 (thyroxine) in CSF (cerebrospinal fluid) ST:STUDY_TITLE and plasma as part of natural diurnal variation ST:STUDY_SUMMARY This study employs targeted LC-MS analysis of CSF and plasma to assess relative ST:STUDY_SUMMARY changes in the levels of thyroid hormone (T3: triiodothyronine and T4: ST:STUDY_SUMMARY thyroxine) at two time points in the diurnal cycle. For this purpose, wild-type ST:STUDY_SUMMARY CD1 mice were kept in a circadian cabinet housing with 12-hour light cycle (7 ST:STUDY_SUMMARY a.m. on/ 7 p.m. off) and tissues were collected consistently at an a.m and a p.m ST:STUDY_SUMMARY time point (9 a.m. and 9 p.m). CSF was collected from adult (3 months old). ST:STUDY_SUMMARY Internal standards (13C-labelled T3 and T4) as well as calibration curves were ST:STUDY_SUMMARY used to estimate the respective T3 and T4 concentration in the examined ST:STUDY_SUMMARY biofluids. ST:INSTITUTE Boston Children's Hospital, Harvard Medical School ST:LABORATORY Kanarek Lab ST:LAST_NAME Petrova ST:FIRST_NAME Boryana ST:ADDRESS Enders 1116.2 300 Longwood Ave ST:EMAIL Boryana.Petrova@childrens.harvard.edu ST:PHONE 6179197352 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 27 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - RF145 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF145 SUBJECT_SAMPLE_FACTORS - RF146 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF146 SUBJECT_SAMPLE_FACTORS - RF147 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF147 SUBJECT_SAMPLE_FACTORS - RF148 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF148 SUBJECT_SAMPLE_FACTORS - RF149 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF149 SUBJECT_SAMPLE_FACTORS - RF150 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF150 SUBJECT_SAMPLE_FACTORS - RF151 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF151 SUBJECT_SAMPLE_FACTORS - RF152 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF152 SUBJECT_SAMPLE_FACTORS - RF153 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF153 SUBJECT_SAMPLE_FACTORS - RF154 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF154 SUBJECT_SAMPLE_FACTORS - RF155 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF155 SUBJECT_SAMPLE_FACTORS - RF156 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF156 SUBJECT_SAMPLE_FACTORS - RF157 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF157 SUBJECT_SAMPLE_FACTORS - RF158 Diurnal_Cycle:PM_CSF (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF158 SUBJECT_SAMPLE_FACTORS - RF159A Diurnal_Cycle:pool RF159-172 1x_A RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF159_p1x SUBJECT_SAMPLE_FACTORS - RF159B Diurnal_Cycle:pool RF159-172 1x_B RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF159_p1xa SUBJECT_SAMPLE_FACTORS - RF159C Diurnal_Cycle:pool RF159-172 1x_C RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF159_p1xb SUBJECT_SAMPLE_FACTORS - RF160A Diurnal_Cycle:pool RF159-172 03x_A RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF160_p03x SUBJECT_SAMPLE_FACTORS - RF160B Diurnal_Cycle:pool RF159-172 03x_B RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF160_p03xa SUBJECT_SAMPLE_FACTORS - RF161A Diurnal_Cycle:pool RF159-172 01x_A RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF161_p01x SUBJECT_SAMPLE_FACTORS - RF161B Diurnal_Cycle:pool RF159-172 01x_B RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF161_p01xa SUBJECT_SAMPLE_FACTORS - RF161C Diurnal_Cycle:pool RF159-172 01x_C RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF161_p01xb SUBJECT_SAMPLE_FACTORS - RF162 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF162 SUBJECT_SAMPLE_FACTORS - RF163 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF163 SUBJECT_SAMPLE_FACTORS - RF164 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF164 SUBJECT_SAMPLE_FACTORS - RF165 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF165 SUBJECT_SAMPLE_FACTORS - RF166 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF166 SUBJECT_SAMPLE_FACTORS - RF167 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF167 SUBJECT_SAMPLE_FACTORS - RF168 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF168 SUBJECT_SAMPLE_FACTORS - RF169 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF169 SUBJECT_SAMPLE_FACTORS - RF170 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF170 SUBJECT_SAMPLE_FACTORS - RF171 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF171 SUBJECT_SAMPLE_FACTORS - RF172A Diurnal_Cycle:pool RF176-185 1x_A RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF172_p1x SUBJECT_SAMPLE_FACTORS - RF172B Diurnal_Cycle:pool RF176-185 1x_B RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF172_p1xa SUBJECT_SAMPLE_FACTORS - RF172C Diurnal_Cycle:pool RF176-185 1x_C RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF172_p1xb SUBJECT_SAMPLE_FACTORS - RF173A Diurnal_Cycle:pool RF176-185 03x_A RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF173_p03x SUBJECT_SAMPLE_FACTORS - RF173B Diurnal_Cycle:pool RF176-185 03x_B RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF173_p03x_20220122111331 SUBJECT_SAMPLE_FACTORS - RF174A Diurnal_Cycle:pool RF176-185 01x_A RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF174_p01x SUBJECT_SAMPLE_FACTORS - RF174B Diurnal_Cycle:pool RF176-185 01x_B RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF174_p01xa SUBJECT_SAMPLE_FACTORS - RF174C Diurnal_Cycle:pool RF176-185 01x_C RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF174_p01xb SUBJECT_SAMPLE_FACTORS - RF175 Diurnal_Cycle:0nM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF175 SUBJECT_SAMPLE_FACTORS - RF176 Diurnal_Cycle:0.2nM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF176 SUBJECT_SAMPLE_FACTORS - RF177 Diurnal_Cycle:2nM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF177 SUBJECT_SAMPLE_FACTORS - RF178 Diurnal_Cycle:20nM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF178 SUBJECT_SAMPLE_FACTORS - RF179 Diurnal_Cycle:200nM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF179 SUBJECT_SAMPLE_FACTORS - RF180 Diurnal_Cycle:2uM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF180 SUBJECT_SAMPLE_FACTORS - RF181 Diurnal_Cycle:20uM T3 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF181 SUBJECT_SAMPLE_FACTORS - RF182 Diurnal_Cycle:0nM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF182 SUBJECT_SAMPLE_FACTORS - RF183 Diurnal_Cycle:0.2nM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF183 SUBJECT_SAMPLE_FACTORS - RF184 Diurnal_Cycle:2nM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF184 SUBJECT_SAMPLE_FACTORS - RF185 Diurnal_Cycle:20nM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF185 SUBJECT_SAMPLE_FACTORS - RF186 Diurnal_Cycle:200nM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF186 SUBJECT_SAMPLE_FACTORS - RF187 Diurnal_Cycle:2uM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF187 SUBJECT_SAMPLE_FACTORS - RF188 Diurnal_Cycle:20uM T4 standard RAW_FILE_NAME=20220121_QEF2_RF_Serum_CSF_RF188 SUBJECT_SAMPLE_FACTORS - RF200 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF200 SUBJECT_SAMPLE_FACTORS - RF201 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF201 SUBJECT_SAMPLE_FACTORS - RF202 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF202 SUBJECT_SAMPLE_FACTORS - RF203 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF203 SUBJECT_SAMPLE_FACTORS - RF204 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF204 SUBJECT_SAMPLE_FACTORS - RF205 Diurnal_Cycle:AM_CSF (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF205 SUBJECT_SAMPLE_FACTORS - RF206 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF206 SUBJECT_SAMPLE_FACTORS - RF207 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF207 SUBJECT_SAMPLE_FACTORS - RF208 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF208 SUBJECT_SAMPLE_FACTORS - RF209 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF209 SUBJECT_SAMPLE_FACTORS - RF210 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF210 SUBJECT_SAMPLE_FACTORS - RF211 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF211 SUBJECT_SAMPLE_FACTORS - RF212 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF212 SUBJECT_SAMPLE_FACTORS - RF213A Diurnal_Cycle:pool CSF RF200-212 1x_A RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF213_CSFpool1xa SUBJECT_SAMPLE_FACTORS - RF213B Diurnal_Cycle:pool CSF RF200-212 1x_B RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF213_CSFpool1xb SUBJECT_SAMPLE_FACTORS - RF213C Diurnal_Cycle:pool CSF RF200-212 1x_C RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF213_CSFpool1xc SUBJECT_SAMPLE_FACTORS - RF214 Diurnal_Cycle:pool CSF RF200-212 03x RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF214_CSFpool03x SUBJECT_SAMPLE_FACTORS - RF215A Diurnal_Cycle:pool CSF RF200-212 01x_A RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF215_CSFpool01xa SUBJECT_SAMPLE_FACTORS - RF215B Diurnal_Cycle:pool CSF RF200-212 01x_B RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF215_CSFpool01xb SUBJECT_SAMPLE_FACTORS - RF216 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF216_20220320130910 SUBJECT_SAMPLE_FACTORS - RF217 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF217_20220320161236 SUBJECT_SAMPLE_FACTORS - RF218 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF218_20220320154940 SUBJECT_SAMPLE_FACTORS - RF219 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF219_20220320165826 SUBJECT_SAMPLE_FACTORS - RF220 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF220_20220320141756 SUBJECT_SAMPLE_FACTORS - RF221 Diurnal_Cycle:AM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF221_20220320163532 SUBJECT_SAMPLE_FACTORS - RF222 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF222_20220320135500 SUBJECT_SAMPLE_FACTORS - RF223 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF223_20220320172122 SUBJECT_SAMPLE_FACTORS - RF224 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF224_20220320124614 SUBJECT_SAMPLE_FACTORS - RF225 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF225_20220320122318 SUBJECT_SAMPLE_FACTORS - RF226 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF226_20220320152644 SUBJECT_SAMPLE_FACTORS - RF227 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF227_20220320133206 SUBJECT_SAMPLE_FACTORS - RF228 Diurnal_Cycle:PM_Serum (TopPhase) RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF228_20220320144052 SUBJECT_SAMPLE_FACTORS - RF229A Diurnal_Cycle:pool serum RF 216-228 1x_A RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF229_pool1xa_20220320113726 SUBJECT_SAMPLE_FACTORS - RF229B Diurnal_Cycle:pool serum RF 216-228 1x_B RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF229_pool1xb_20220320150348 SUBJECT_SAMPLE_FACTORS - RF229C Diurnal_Cycle:pool serum RF 216-228 1x_C RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF229_pool1xc_20220320174418 SUBJECT_SAMPLE_FACTORS - RF230 Diurnal_Cycle:pool serum RF 216-228 03x RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF230_pool03x_20220320180714 SUBJECT_SAMPLE_FACTORS - RF231A Diurnal_Cycle:pool serum RF 216-228 01x_A RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF231_pool01a_20220320120022 SUBJECT_SAMPLE_FACTORS - RF231B Diurnal_Cycle:pool serum RF 216-228 01x_B RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_RF231_pool01b_20220320183010 SUBJECT_SAMPLE_FACTORS - RF175B Diurnal_Cycle:0nM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_01 SUBJECT_SAMPLE_FACTORS - RF176B Diurnal_Cycle:0.2nM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_02 SUBJECT_SAMPLE_FACTORS - RF177B Diurnal_Cycle:2nM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_03 SUBJECT_SAMPLE_FACTORS - RF178B Diurnal_Cycle:20nM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_04 SUBJECT_SAMPLE_FACTORS - RF179B Diurnal_Cycle:200nM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_05 SUBJECT_SAMPLE_FACTORS - RF180B Diurnal_Cycle:2uM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_06 SUBJECT_SAMPLE_FACTORS - RF181B Diurnal_Cycle:20uM T3 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T3_07 SUBJECT_SAMPLE_FACTORS - RF182B Diurnal_Cycle:0nM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_01 SUBJECT_SAMPLE_FACTORS - RF183B Diurnal_Cycle:0.2nM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_02 SUBJECT_SAMPLE_FACTORS - RF184B Diurnal_Cycle:2nM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_03 SUBJECT_SAMPLE_FACTORS - RF185B Diurnal_Cycle:20nM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_04 SUBJECT_SAMPLE_FACTORS - RF186B Diurnal_Cycle:200nM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_05 SUBJECT_SAMPLE_FACTORS - RF187B Diurnal_Cycle:2uM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_06 SUBJECT_SAMPLE_FACTORS - RF188B Diurnal_Cycle:20uM T4 standard RAW_FILE_NAME=20220318_QEF2_C18_T3T4narrow_T4_07 #COLLECTION CO:COLLECTION_SUMMARY All animal studies were performed under the protocol approved by the CO:COLLECTION_SUMMARY Institutional Animal Care and Use Committee (IACUC) of Boston Children’s CO:COLLECTION_SUMMARY Hospital (BCH). All mice were housed in a 12h light-dark cycle with ad libitum CO:COLLECTION_SUMMARY access to food and water. CSF, eCSF, was collected from the cisterna magna of CO:COLLECTION_SUMMARY the pup embryos and mother, and centrifuged at 5,000g for 10 min. at 4 °C to CO:COLLECTION_SUMMARY remove any tissue debris. CSF samples were kept on ice and analyzed the same day CO:COLLECTION_SUMMARY as collection. CO:SAMPLE_TYPE CSF #TREATMENT TR:TREATMENT_SUMMARY Mice (CD-1 males) kept in circadian cabinet housing with 12-hour light cycle (7 TR:TREATMENT_SUMMARY a.m. on/ 7 p.m. off). #SAMPLEPREP SP:SAMPLEPREP_SUMMARY CSF was collected from adult (3 months old) wild-type CD1 mice. Samples were SP:SAMPLEPREP_SUMMARY placed on wet ice, then spun 1000xg for 10 minutes at 4C. The supernatant was SP:SAMPLEPREP_SUMMARY collected. Per condition, 5-10µL of fresh, cleared CSF or 5µl serum was SP:SAMPLEPREP_SUMMARY extracted in 4:6:3 chlorophorm:methanol:water mixture supplemented with SP:SAMPLEPREP_SUMMARY isotopically labeled T3 and T4 (Cambridge Isotope Laboratories, CLM-7185-C and SP:SAMPLEPREP_SUMMARY CLM-8931-PK ) as well as isotopically labelled 17 amino acids and isotopically SP:SAMPLEPREP_SUMMARY labelled reduced glutathione (Cambridge Isotope Laboratories, MSK-A2-1.2 and SP:SAMPLEPREP_SUMMARY CNLM-6245-10). After centrifugation for 10 min at maximum speed on a benchtop SP:SAMPLEPREP_SUMMARY centrifuge (Eppendorf) the top, hydrophilic layer (top phase) was transferred to SP:SAMPLEPREP_SUMMARY a new tube, dried using a nitrogen dryer and reconstituted in 20 µl water SP:SAMPLEPREP_SUMMARY (supplemented with QReSS, Cambridge Isotope Laboratories, MSK-QRESS-KIT) by SP:SAMPLEPREP_SUMMARY brief vortexing. Extracted metabolites were spun again and cleared supernatant SP:SAMPLEPREP_SUMMARY was transferred to LC-MS micro vials. A small amount of each sample was pooled SP:SAMPLEPREP_SUMMARY and serially diluted 3- and 10-fold to be used as quality controls throughout SP:SAMPLEPREP_SUMMARY the run of each batch. I calibration curve of unlabeled T3 and T4 standards was SP:SAMPLEPREP_SUMMARY run per experiment for concentration calculations. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Ascentis Express C18 HPLC column (2.7 μm × 15 cm × 2.1 mm; CH:CHROMATOGRAPHY_SUMMARY Sigma Aldrich). CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Ascentis Express C18 (150 x 2.1mm,2.7um) CH:SOLVENT_A water, 0.1% formic acid CH:SOLVENT_B acetonitrile, 0.1% formic acid CH:FLOW_GRADIENT 0–5 min: gradient was held at 5% B; 2–12.1 min: linear gradient of 5% to CH:FLOW_GRADIENT 95% B; 12.1–17.0 min: 95% B; 17.1–21.0 min: gradient was returned to 5% CH:FLOW_GRADIENT B CH:FLOW_RATE 0.250 ml/min CH:COLUMN_TEMPERATURE 30 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Plus Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS MS data acquisition was performed using a QExactive benchtop orbitrap mass MS:MS_COMMENTS spectrometer equipped with an Ion Max source and a HESI II probe (Thermo Fisher MS:MS_COMMENTS Scientific, San Jose, CA) and was performed at a narrow scan in positive mode MS:MS_COMMENTS (m/z = 600-800) for more specific detection of thyroxine hormones, the MS:MS_COMMENTS resolution was set at 70,000, the AGC target was 5x105, and the max IT was 100 MS:MS_COMMENTS msec. HESI conditions were: Sheath gas flow rate: 40; Aug gas flow rate: 10; MS:MS_COMMENTS Sweet gas flow rate: 0; Spray voltage: 3.5kV (pos), 2.8kV (neg); Capillary MS:MS_COMMENTS temperature: 380ºC; S-lens RF: 60; Aux gas heater temperature: 420 ºC. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS nM MS_METABOLITE_DATA_START Samples RF145 RF146 RF147 RF148 RF149 RF150 RF151 RF152 RF153 RF154 RF155 RF156 RF157 RF158 RF200 RF201 RF202 RF203 RF204 RF205 RF206 RF207 RF208 RF209 RF210 RF211 RF212 RF162 RF163 RF164 RF165 RF166 RF167 RF168 RF169 RF170 RF171 RF216 RF217 RF218 RF219 RF220 RF221 RF222 RF223 RF224 RF225 RF226 RF227 RF228 Factors Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:PM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:AM_CSF (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:AM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) Diurnal_Cycle:PM_Serum (TopPhase) thyroxine 0.741803329 0.755974521 0.643176884 0.353147734 0.182803996 NA 1.135387896 1.17753791 1.374849535 0.248019977 1.236778246 0.073942534 1.01776372 1.261740121 0.171935193 0.230293228 0.180602581 0.126565361 0.09869018 0.108785255 0.050565145 0.238487644 0.124968696 0.177164288 0.096308331 NA NA 67.63816808 32.8619847 40.01393126 63.45660565 22.39931616 56.24839158 18.2161656 49.90229765 64.72732584 88.31161281 13.26603972 6.569466291 6.963683285 13.32390739 9.968174285 13.42792551 29.61472157 13.92098167 13.29093456 5.90447333 27.76045159 16.81662331 14.80487412 triiodothyronine NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1.229673548 1.717151043 0.975502451 1.643974987 1.74211678 1.818374804 2.054610555 1.699947083 1.812747586 1.82694651 2.177670861 3.809491148 2.98384153 NA NA NA NA NA NA NA NA NA NA 3.403350774 4.004768262 3.191851248 3.721256973 5.451477911 1.114151304 3.057786406 2.885830331 3.566307481 4.162980425 3.708463019 5.439627145 4.230248166 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name chemical formula PubChem KEGG m/z RT thyroxine C15H11I4NO4 5819 C01829 777.694 8.79 triiodothyronine C15H12I3NO4 5920 C02465 651.7973 8.38 METABOLITES_END #END