{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002707","ANALYSIS_ID":"AN004389","VERSION":"1","CREATED_ON":"May 19, 2023, 11:32 am"},

"PROJECT":{"PROJECT_TITLE":"Combining multi-omics and real-time optics to track diurnal transitions in the choroid plexus and CSF at molecular, spatial, and temporal resolution","PROJECT_SUMMARY":"The choroid plexus (ChP) comprises the blood-CSF barrier and regulates cerebrospinal fluid (CSF) composition. Details of ChP-CSF regulation throughout the day remain unknown, largely due to lack of tools. We developed a platform for analyzing diurnal variations in mouse ChP function. We demonstrate widespread diurnal regulation of ChP secretion and barrier function across hours during the circadian day and in response to feeding cues, resulting in changes in CSF composition. ChP metabolomics uncovered increased dark phase oxidation. Transthyretin (TTR), a thyroid hormone chaperone, exhibited strong diurnal regulation and CSF-TTR levels varied across the day in register with CSF thyroid hormone levels and ChP-TTR expression. Our data will serve as a resource for the community, enabling better understanding of circadian rhythms and ChP diurnal function and regulation.","INSTITUTE":"Boston Childrens Hospital","DEPARTMENT":"Pathology","LABORATORY":"Kanarek Lab","LAST_NAME":"Petrova","FIRST_NAME":"Boryana","ADDRESS":"300 Longwood Av, Boston, MA, 2115, USA","EMAIL":"boryana.petrova@childrens.harvard.edu","PHONE":"6173557433","CONTRIBUTORS":"Boryana Petrova, Ryann Fame"},

"STUDY":{"STUDY_TITLE":"Levels of T3 (triiodothyronine) and T4 (thyroxine) in CSF (cerebrospinal fluid) and plasma as part of natural diurnal variation","STUDY_SUMMARY":"This study employs targeted LC-MS analysis of CSF and plasma to assess relative changes in the levels of thyroid hormone (T3: triiodothyronine and T4: thyroxine) at two time points in the diurnal cycle. For this purpose, wild-type CD1 mice were kept in a circadian cabinet housing with 12-hour light cycle (7 a.m. on/ 7 p.m. off) and tissues were collected consistently at an a.m and a p.m time point (9 a.m. and 9 p.m). CSF was collected from adult (3 months old). Internal standards (13C-labelled T3 and T4) as well as calibration curves were used to estimate the respective T3 and T4 concentration in the examined biofluids.","INSTITUTE":"Boston Children's Hospital, Harvard Medical School","LABORATORY":"Kanarek Lab","LAST_NAME":"Petrova","FIRST_NAME":"Boryana","ADDRESS":"Enders 1116.2 300 Longwood Ave","EMAIL":"Boryana.Petrova@childrens.harvard.edu","PHONE":"6179197352","NUM_GROUPS":"2","TOTAL_SUBJECTS":"27"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"RF145",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF145"}
},
{
"Subject ID":"-",
"Sample ID":"RF146",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF146"}
},
{
"Subject ID":"-",
"Sample ID":"RF147",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF147"}
},
{
"Subject ID":"-",
"Sample ID":"RF148",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF148"}
},
{
"Subject ID":"-",
"Sample ID":"RF149",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF149"}
},
{
"Subject ID":"-",
"Sample ID":"RF150",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF150"}
},
{
"Subject ID":"-",
"Sample ID":"RF151",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF151"}
},
{
"Subject ID":"-",
"Sample ID":"RF152",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF152"}
},
{
"Subject ID":"-",
"Sample ID":"RF153",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF153"}
},
{
"Subject ID":"-",
"Sample ID":"RF154",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF154"}
},
{
"Subject ID":"-",
"Sample ID":"RF155",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF155"}
},
{
"Subject ID":"-",
"Sample ID":"RF156",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF156"}
},
{
"Subject ID":"-",
"Sample ID":"RF157",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF157"}
},
{
"Subject ID":"-",
"Sample ID":"RF158",
"Factors":{"Diurnal_Cycle":"PM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF158"}
},
{
"Subject ID":"-",
"Sample ID":"RF159A",
"Factors":{"Diurnal_Cycle":"pool RF159-172 1x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF159_p1x"}
},
{
"Subject ID":"-",
"Sample ID":"RF159B",
"Factors":{"Diurnal_Cycle":"pool RF159-172 1x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF159_p1xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF159C",
"Factors":{"Diurnal_Cycle":"pool RF159-172 1x_C"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF159_p1xb"}
},
{
"Subject ID":"-",
"Sample ID":"RF160A",
"Factors":{"Diurnal_Cycle":"pool RF159-172 03x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF160_p03x"}
},
{
"Subject ID":"-",
"Sample ID":"RF160B",
"Factors":{"Diurnal_Cycle":"pool RF159-172 03x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF160_p03xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF161A",
"Factors":{"Diurnal_Cycle":"pool RF159-172 01x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF161_p01x"}
},
{
"Subject ID":"-",
"Sample ID":"RF161B",
"Factors":{"Diurnal_Cycle":"pool RF159-172 01x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF161_p01xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF161C",
"Factors":{"Diurnal_Cycle":"pool RF159-172 01x_C"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF161_p01xb"}
},
{
"Subject ID":"-",
"Sample ID":"RF162",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF162"}
},
{
"Subject ID":"-",
"Sample ID":"RF163",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF163"}
},
{
"Subject ID":"-",
"Sample ID":"RF164",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF164"}
},
{
"Subject ID":"-",
"Sample ID":"RF165",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF165"}
},
{
"Subject ID":"-",
"Sample ID":"RF166",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF166"}
},
{
"Subject ID":"-",
"Sample ID":"RF167",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF167"}
},
{
"Subject ID":"-",
"Sample ID":"RF168",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF168"}
},
{
"Subject ID":"-",
"Sample ID":"RF169",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF169"}
},
{
"Subject ID":"-",
"Sample ID":"RF170",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF170"}
},
{
"Subject ID":"-",
"Sample ID":"RF171",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF171"}
},
{
"Subject ID":"-",
"Sample ID":"RF172A",
"Factors":{"Diurnal_Cycle":"pool RF176-185 1x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF172_p1x"}
},
{
"Subject ID":"-",
"Sample ID":"RF172B",
"Factors":{"Diurnal_Cycle":"pool RF176-185 1x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF172_p1xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF172C",
"Factors":{"Diurnal_Cycle":"pool RF176-185 1x_C"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF172_p1xb"}
},
{
"Subject ID":"-",
"Sample ID":"RF173A",
"Factors":{"Diurnal_Cycle":"pool RF176-185 03x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF173_p03x"}
},
{
"Subject ID":"-",
"Sample ID":"RF173B",
"Factors":{"Diurnal_Cycle":"pool RF176-185 03x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF173_p03x_20220122111331"}
},
{
"Subject ID":"-",
"Sample ID":"RF174A",
"Factors":{"Diurnal_Cycle":"pool RF176-185 01x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF174_p01x"}
},
{
"Subject ID":"-",
"Sample ID":"RF174B",
"Factors":{"Diurnal_Cycle":"pool RF176-185 01x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF174_p01xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF174C",
"Factors":{"Diurnal_Cycle":"pool RF176-185 01x_C"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF174_p01xb"}
},
{
"Subject ID":"-",
"Sample ID":"RF175",
"Factors":{"Diurnal_Cycle":"0nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF175"}
},
{
"Subject ID":"-",
"Sample ID":"RF176",
"Factors":{"Diurnal_Cycle":"0.2nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF176"}
},
{
"Subject ID":"-",
"Sample ID":"RF177",
"Factors":{"Diurnal_Cycle":"2nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF177"}
},
{
"Subject ID":"-",
"Sample ID":"RF178",
"Factors":{"Diurnal_Cycle":"20nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF178"}
},
{
"Subject ID":"-",
"Sample ID":"RF179",
"Factors":{"Diurnal_Cycle":"200nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF179"}
},
{
"Subject ID":"-",
"Sample ID":"RF180",
"Factors":{"Diurnal_Cycle":"2uM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF180"}
},
{
"Subject ID":"-",
"Sample ID":"RF181",
"Factors":{"Diurnal_Cycle":"20uM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF181"}
},
{
"Subject ID":"-",
"Sample ID":"RF182",
"Factors":{"Diurnal_Cycle":"0nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF182"}
},
{
"Subject ID":"-",
"Sample ID":"RF183",
"Factors":{"Diurnal_Cycle":"0.2nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF183"}
},
{
"Subject ID":"-",
"Sample ID":"RF184",
"Factors":{"Diurnal_Cycle":"2nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF184"}
},
{
"Subject ID":"-",
"Sample ID":"RF185",
"Factors":{"Diurnal_Cycle":"20nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF185"}
},
{
"Subject ID":"-",
"Sample ID":"RF186",
"Factors":{"Diurnal_Cycle":"200nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF186"}
},
{
"Subject ID":"-",
"Sample ID":"RF187",
"Factors":{"Diurnal_Cycle":"2uM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF187"}
},
{
"Subject ID":"-",
"Sample ID":"RF188",
"Factors":{"Diurnal_Cycle":"20uM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220121_QEF2_RF_Serum_CSF_RF188"}
},
{
"Subject ID":"-",
"Sample ID":"RF200",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF200"}
},
{
"Subject ID":"-",
"Sample ID":"RF201",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF201"}
},
{
"Subject ID":"-",
"Sample ID":"RF202",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF202"}
},
{
"Subject ID":"-",
"Sample ID":"RF203",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF203"}
},
{
"Subject ID":"-",
"Sample ID":"RF204",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF204"}
},
{
"Subject ID":"-",
"Sample ID":"RF205",
"Factors":{"Diurnal_Cycle":"AM_CSF (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF205"}
},
{
"Subject ID":"-",
"Sample ID":"RF206",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF206"}
},
{
"Subject ID":"-",
"Sample ID":"RF207",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF207"}
},
{
"Subject ID":"-",
"Sample ID":"RF208",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF208"}
},
{
"Subject ID":"-",
"Sample ID":"RF209",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF209"}
},
{
"Subject ID":"-",
"Sample ID":"RF210",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF210"}
},
{
"Subject ID":"-",
"Sample ID":"RF211",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF211"}
},
{
"Subject ID":"-",
"Sample ID":"RF212",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF212"}
},
{
"Subject ID":"-",
"Sample ID":"RF213A",
"Factors":{"Diurnal_Cycle":"pool CSF RF200-212 1x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF213_CSFpool1xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF213B",
"Factors":{"Diurnal_Cycle":"pool CSF RF200-212 1x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF213_CSFpool1xb"}
},
{
"Subject ID":"-",
"Sample ID":"RF213C",
"Factors":{"Diurnal_Cycle":"pool CSF RF200-212 1x_C"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF213_CSFpool1xc"}
},
{
"Subject ID":"-",
"Sample ID":"RF214",
"Factors":{"Diurnal_Cycle":"pool CSF RF200-212 03x"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF214_CSFpool03x"}
},
{
"Subject ID":"-",
"Sample ID":"RF215A",
"Factors":{"Diurnal_Cycle":"pool CSF RF200-212 01x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF215_CSFpool01xa"}
},
{
"Subject ID":"-",
"Sample ID":"RF215B",
"Factors":{"Diurnal_Cycle":"pool CSF RF200-212 01x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF215_CSFpool01xb"}
},
{
"Subject ID":"-",
"Sample ID":"RF216",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF216_20220320130910"}
},
{
"Subject ID":"-",
"Sample ID":"RF217",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF217_20220320161236"}
},
{
"Subject ID":"-",
"Sample ID":"RF218",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF218_20220320154940"}
},
{
"Subject ID":"-",
"Sample ID":"RF219",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF219_20220320165826"}
},
{
"Subject ID":"-",
"Sample ID":"RF220",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF220_20220320141756"}
},
{
"Subject ID":"-",
"Sample ID":"RF221",
"Factors":{"Diurnal_Cycle":"AM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF221_20220320163532"}
},
{
"Subject ID":"-",
"Sample ID":"RF222",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF222_20220320135500"}
},
{
"Subject ID":"-",
"Sample ID":"RF223",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF223_20220320172122"}
},
{
"Subject ID":"-",
"Sample ID":"RF224",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF224_20220320124614"}
},
{
"Subject ID":"-",
"Sample ID":"RF225",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF225_20220320122318"}
},
{
"Subject ID":"-",
"Sample ID":"RF226",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF226_20220320152644"}
},
{
"Subject ID":"-",
"Sample ID":"RF227",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF227_20220320133206"}
},
{
"Subject ID":"-",
"Sample ID":"RF228",
"Factors":{"Diurnal_Cycle":"PM_Serum (TopPhase)"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF228_20220320144052"}
},
{
"Subject ID":"-",
"Sample ID":"RF229A",
"Factors":{"Diurnal_Cycle":"pool serum RF 216-228 1x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF229_pool1xa_20220320113726"}
},
{
"Subject ID":"-",
"Sample ID":"RF229B",
"Factors":{"Diurnal_Cycle":"pool serum RF 216-228 1x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF229_pool1xb_20220320150348"}
},
{
"Subject ID":"-",
"Sample ID":"RF229C",
"Factors":{"Diurnal_Cycle":"pool serum RF 216-228 1x_C"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF229_pool1xc_20220320174418"}
},
{
"Subject ID":"-",
"Sample ID":"RF230",
"Factors":{"Diurnal_Cycle":"pool serum RF 216-228 03x"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF230_pool03x_20220320180714"}
},
{
"Subject ID":"-",
"Sample ID":"RF231A",
"Factors":{"Diurnal_Cycle":"pool serum RF 216-228 01x_A"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF231_pool01a_20220320120022"}
},
{
"Subject ID":"-",
"Sample ID":"RF231B",
"Factors":{"Diurnal_Cycle":"pool serum RF 216-228 01x_B"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_RF231_pool01b_20220320183010"}
},
{
"Subject ID":"-",
"Sample ID":"RF175B",
"Factors":{"Diurnal_Cycle":"0nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_01"}
},
{
"Subject ID":"-",
"Sample ID":"RF176B",
"Factors":{"Diurnal_Cycle":"0.2nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_02"}
},
{
"Subject ID":"-",
"Sample ID":"RF177B",
"Factors":{"Diurnal_Cycle":"2nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_03"}
},
{
"Subject ID":"-",
"Sample ID":"RF178B",
"Factors":{"Diurnal_Cycle":"20nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_04"}
},
{
"Subject ID":"-",
"Sample ID":"RF179B",
"Factors":{"Diurnal_Cycle":"200nM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_05"}
},
{
"Subject ID":"-",
"Sample ID":"RF180B",
"Factors":{"Diurnal_Cycle":"2uM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_06"}
},
{
"Subject ID":"-",
"Sample ID":"RF181B",
"Factors":{"Diurnal_Cycle":"20uM T3 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T3_07"}
},
{
"Subject ID":"-",
"Sample ID":"RF182B",
"Factors":{"Diurnal_Cycle":"0nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_01"}
},
{
"Subject ID":"-",
"Sample ID":"RF183B",
"Factors":{"Diurnal_Cycle":"0.2nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_02"}
},
{
"Subject ID":"-",
"Sample ID":"RF184B",
"Factors":{"Diurnal_Cycle":"2nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_03"}
},
{
"Subject ID":"-",
"Sample ID":"RF185B",
"Factors":{"Diurnal_Cycle":"20nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_04"}
},
{
"Subject ID":"-",
"Sample ID":"RF186B",
"Factors":{"Diurnal_Cycle":"200nM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_05"}
},
{
"Subject ID":"-",
"Sample ID":"RF187B",
"Factors":{"Diurnal_Cycle":"2uM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_06"}
},
{
"Subject ID":"-",
"Sample ID":"RF188B",
"Factors":{"Diurnal_Cycle":"20uM T4 standard"},
"Additional sample data":{"RAW_FILE_NAME":"20220318_QEF2_C18_T3T4narrow_T4_07"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"All animal studies were performed under the protocol approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital (BCH). All mice were housed in a 12h light-dark cycle with ad libitum access to food and water. CSF, eCSF, was collected from the cisterna magna of the pup embryos and mother, and centrifuged at 5,000g for 10 min. at 4 °C to remove any tissue debris. CSF samples were kept on ice and analyzed the same day as collection.","SAMPLE_TYPE":"CSF"},

"TREATMENT":{"TREATMENT_SUMMARY":"Mice (CD-1 males) kept in circadian cabinet housing with 12-hour light cycle (7 a.m. on/ 7 p.m. off)."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"CSF was collected from adult (3 months old) wild-type CD1 mice. Samples were placed on wet ice, then spun 1000xg for 10 minutes at 4C. The supernatant was collected. Per condition, 5-10µL of fresh, cleared CSF or 5µl serum was extracted in 4:6:3 chlorophorm:methanol:water mixture supplemented with isotopically labeled T3 and T4 (Cambridge Isotope Laboratories, CLM-7185-C and CLM-8931-PK ) as well as isotopically labelled 17 amino acids and isotopically labelled reduced glutathione (Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). After centrifugation for 10 min at maximum speed on a benchtop centrifuge (Eppendorf) the top, hydrophilic layer (top phase) was transferred to a new tube, dried using a nitrogen dryer and reconstituted in 20 µl water (supplemented with QReSS, Cambridge Isotope Laboratories, MSK-QRESS-KIT) by brief vortexing. Extracted metabolites were spun again and cleared supernatant was transferred to LC-MS micro vials. A small amount of each sample was pooled and serially diluted 3- and 10-fold to be used as quality controls throughout the run of each batch. I calibration curve of unlabeled T3 and T4 standards was run per experiment for concentration calculations."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Ascentis Express C18 HPLC column (2.7 μm × 15 cm × 2.1 mm; Sigma Aldrich).","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Ascentis Express C18 (150 x 2.1mm,2.7um)","SOLVENT_A":"water, 0.1% formic acid","SOLVENT_B":"acetonitrile, 0.1% formic acid","FLOW_GRADIENT":"0–5 min: gradient was held at 5% B; 2–12.1 min: linear gradient of 5% to 95% B; 12.1–17.0 min: 95% B; 17.1–21.0 min: gradient was returned to 5% B","FLOW_RATE":"0.250 ml/min","COLUMN_TEMPERATURE":"30"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"MS data acquisition was performed using a QExactive benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe (Thermo Fisher Scientific, San Jose, CA) and was performed at a narrow scan in positive mode (m/z = 600-800) for more specific detection of thyroxine hormones, the resolution was set at 70,000, the AGC target was 5x105, and the max IT was 100 msec. HESI conditions were: Sheath gas flow rate: 40; Aug gas flow rate: 10; Sweet gas flow rate: 0; Spray voltage: 3.5kV (pos), 2.8kV (neg); Capillary temperature: 380ºC; S-lens RF: 60; Aux gas heater temperature: 420 ºC."},

"MS_METABOLITE_DATA":{
"Units":"nM",

"Data":[{"Metabolite":"thyroxine","RF145":"0.741803329","RF146":"0.755974521","RF147":"0.643176884","RF148":"0.353147734","RF149":"0.182803996","RF150":"NA","RF151":"1.135387896","RF152":"1.17753791","RF153":"1.374849535","RF154":"0.248019977","RF155":"1.236778246","RF156":"0.073942534","RF157":"1.01776372","RF158":"1.261740121","RF200":"0.171935193","RF201":"0.230293228","RF202":"0.180602581","RF203":"0.126565361","RF204":"0.09869018","RF205":"0.108785255","RF206":"0.050565145","RF207":"0.238487644","RF208":"0.124968696","RF209":"0.177164288","RF210":"0.096308331","RF211":"NA","RF212":"NA","RF162":"67.63816808","RF163":"32.8619847","RF164":"40.01393126","RF165":"63.45660565","RF166":"22.39931616","RF167":"56.24839158","RF168":"18.2161656","RF169":"49.90229765","RF170":"64.72732584","RF171":"88.31161281","RF216":"13.26603972","RF217":"6.569466291","RF218":"6.963683285","RF219":"13.32390739","RF220":"9.968174285","RF221":"13.42792551","RF222":"29.61472157","RF223":"13.92098167","RF224":"13.29093456","RF225":"5.90447333","RF226":"27.76045159","RF227":"16.81662331","RF228":"14.80487412"},{"Metabolite":"triiodothyronine","RF145":"NA","RF146":"NA","RF147":"NA","RF148":"NA","RF149":"NA","RF150":"NA","RF151":"NA","RF152":"NA","RF153":"NA","RF154":"NA","RF155":"NA","RF156":"NA","RF157":"NA","RF158":"NA","RF200":"1.229673548","RF201":"1.717151043","RF202":"0.975502451","RF203":"1.643974987","RF204":"1.74211678","RF205":"1.818374804","RF206":"2.054610555","RF207":"1.699947083","RF208":"1.812747586","RF209":"1.82694651","RF210":"2.177670861","RF211":"3.809491148","RF212":"2.98384153","RF162":"NA","RF163":"NA","RF164":"NA","RF165":"NA","RF166":"NA","RF167":"NA","RF168":"NA","RF169":"NA","RF170":"NA","RF171":"NA","RF216":"3.403350774","RF217":"4.004768262","RF218":"3.191851248","RF219":"3.721256973","RF220":"5.451477911","RF221":"1.114151304","RF222":"3.057786406","RF223":"2.885830331","RF224":"3.566307481","RF225":"4.162980425","RF226":"3.708463019","RF227":"5.439627145","RF228":"4.230248166"}],

"Metabolites":[{"Metabolite":"thyroxine","chemical formula":"C15H11I4NO4","PubChem":"5819","KEGG":"C01829","m/z":"777.694","RT":"8.79"},{"Metabolite":"triiodothyronine","chemical formula":"C15H12I3NO4","PubChem":"5920","KEGG":"C02465","m/z":"651.7973","RT":"8.38"}]
}

}