#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