#METABOLOMICS WORKBENCH RDOKO28_20231213_070552 DATATRACK_ID:4507 STUDY_ID:ST003003 ANALYSIS_ID:AN004934 PROJECT_ID:PR001872 VERSION 1 CREATED_ON December 13, 2023, 9:00 pm #PROJECT PR:PROJECT_TITLE Gut microbiota and metabolites in estrus cycle and their changes in a menopausal PR:PROJECT_TITLE transition rat model with typical neuroendocrine aging PR:PROJECT_SUMMARY Neuroendocrine alterations in the mid-life hypothalamus coupled with PR:PROJECT_SUMMARY reproductive decline herald the initiation of menopausal transition. The certain PR:PROJECT_SUMMARY feature and contribution of gut microflora and metabolites to neuroendocrine PR:PROJECT_SUMMARY changes in the menopausal transition remain largely unknown. Fecal samples of PR:PROJECT_SUMMARY rats experiencing different reproductive stages were collected and processed for PR:PROJECT_SUMMARY 16S rRNA and liquid chromatography-mass spectrometry sequencing. The differences PR:PROJECT_SUMMARY of gut microbiota and metabolites between young and middle-aged rats during PR:PROJECT_SUMMARY proestrus and diestrus were analyzed and their relationships to neuroendocrine PR:PROJECT_SUMMARY aging were then examined. This study documents specific gut microbial PR:PROJECT_SUMMARY composition changes and concomitant shifting trends of metabolites during PR:PROJECT_SUMMARY menopausal transition, which may initiate the gut-brain dysfunction in PR:PROJECT_SUMMARY neuroendocrine aging. PR:INSTITUTE Fudan University PR:LAST_NAME Dai PR:FIRST_NAME Ruoxi PR:ADDRESS 128 Shenyang Road PR:EMAIL rqdai21@m.fudan.edu.cn PR:PHONE +86-21-33189900 #STUDY ST:STUDY_TITLE Gut microbiota and metabolites in estrus cycle and their changes in a menopausal ST:STUDY_TITLE transition rat model with typical neuroendocrine aging ST:STUDY_SUMMARY Neuroendocrine alterations in the mid-life hypothalamus coupled with ST:STUDY_SUMMARY reproductive decline herald the initiation of menopausal transition. The certain ST:STUDY_SUMMARY feature and contribution of gut microflora and metabolites to neuroendocrine ST:STUDY_SUMMARY changes in the menopausal transition remain largely unknown. Fecal samples of ST:STUDY_SUMMARY rats experiencing different reproductive stages were collected and processed for ST:STUDY_SUMMARY 16S rRNA and liquid chromatography-mass spectrometry sequencing. The differences ST:STUDY_SUMMARY of gut microbiota and metabolites between young and middle-aged rats during ST:STUDY_SUMMARY proestrus and diestrus were analyzed and their relationships to neuroendocrine ST:STUDY_SUMMARY aging were then examined. This study documents specific gut microbial ST:STUDY_SUMMARY composition changes and concomitant shifting trends of metabolites during ST:STUDY_SUMMARY menopausal transition, which may initiate the gut-brain dysfunction in ST:STUDY_SUMMARY neuroendocrine aging. ST:INSTITUTE Fudan University ST:LAST_NAME Dai ST:FIRST_NAME Ruoxi ST:ADDRESS 128 Shenyang Road ST:EMAIL rqdai21@m.fudan.edu.cn ST:PHONE +86-21-33189900 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Rattus norvegicus SU:TAXONOMY_ID 10116 #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 - MA1 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA1-neg.raw; RAW_FILE_NAME=MA1-pos.raw SUBJECT_SAMPLE_FACTORS - MA4 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA4-neg.raw; RAW_FILE_NAME=MA4-pos.raw SUBJECT_SAMPLE_FACTORS - MA6 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA6-neg.raw; RAW_FILE_NAME=MA6-pos.raw SUBJECT_SAMPLE_FACTORS - MA7 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA7-neg.raw; RAW_FILE_NAME=MA7-pos.raw SUBJECT_SAMPLE_FACTORS - MA13 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA13-neg.raw; RAW_FILE_NAME=MA13-pos.raw SUBJECT_SAMPLE_FACTORS - MA26 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA26-neg.raw; RAW_FILE_NAME=MA26-pos.raw SUBJECT_SAMPLE_FACTORS - MA34 Age:9-10 months | Estrus Stage:Proestrus RAW_FILE_NAME=MA34-neg.raw; RAW_FILE_NAME=MA34-pos.raw SUBJECT_SAMPLE_FACTORS - MA5 Age:9-10 months | Estrus Stage:Diestrus RAW_FILE_NAME=MA5-neg.raw; RAW_FILE_NAME=MA5-pos.raw SUBJECT_SAMPLE_FACTORS - MA25 Age:9-10 months | Estrus Stage:Diestrus RAW_FILE_NAME=MA25-neg.raw; RAW_FILE_NAME=MA25-pos.raw SUBJECT_SAMPLE_FACTORS - MA28 Age:9-10 months | Estrus Stage:Diestrus RAW_FILE_NAME=MA28-neg.raw; RAW_FILE_NAME=MA28-pos.raw SUBJECT_SAMPLE_FACTORS - MA17 Age:9-10 months | Estrus Stage:Diestrus RAW_FILE_NAME=MA17-neg.raw; RAW_FILE_NAME=MA17-pos.raw SUBJECT_SAMPLE_FACTORS - MA21 Age:9-10 months | Estrus Stage:Diestrus RAW_FILE_NAME=MA21-neg.raw; RAW_FILE_NAME=MA21-pos.raw SUBJECT_SAMPLE_FACTORS - Y7 Age:2-3 months | Estrus Stage:Proestrus RAW_FILE_NAME=Y7-neg.raw; RAW_FILE_NAME=Y7-pos.raw SUBJECT_SAMPLE_FACTORS - Y9 Age:2-3 months | Estrus Stage:Proestrus RAW_FILE_NAME=Y9-neg.raw; RAW_FILE_NAME=Y9-pos.raw SUBJECT_SAMPLE_FACTORS - Y13 Age:2-3 months | Estrus Stage:Proestrus RAW_FILE_NAME=Y13-neg.raw; RAW_FILE_NAME=Y13-pos.raw SUBJECT_SAMPLE_FACTORS - Y5 Age:2-3 months | Estrus Stage:Proestrus RAW_FILE_NAME=Y5-neg.raw; RAW_FILE_NAME=Y5-pos.raw SUBJECT_SAMPLE_FACTORS - Y8 Age:2-3 months | Estrus Stage:Proestrus RAW_FILE_NAME=Y8-neg.raw; RAW_FILE_NAME=Y8-pos.raw SUBJECT_SAMPLE_FACTORS - Y1 Age:2-3 months | Estrus Stage:Diestrus RAW_FILE_NAME=Y1-neg.raw; RAW_FILE_NAME=Y1-pos.raw SUBJECT_SAMPLE_FACTORS - Y3 Age:2-3 months | Estrus Stage:Diestrus RAW_FILE_NAME=Y3-neg.raw; RAW_FILE_NAME=Y3-pos.raw SUBJECT_SAMPLE_FACTORS - Y4 Age:2-3 months | Estrus Stage:Diestrus RAW_FILE_NAME=Y4-neg.raw; RAW_FILE_NAME=Y4-pos.raw SUBJECT_SAMPLE_FACTORS - Y6 Age:2-3 months | Estrus Stage:Diestrus RAW_FILE_NAME=Y6-neg.raw; RAW_FILE_NAME=Y6-pos.raw SUBJECT_SAMPLE_FACTORS - Y10 Age:2-3 months | Estrus Stage:Diestrus RAW_FILE_NAME=Y10-neg.raw; RAW_FILE_NAME=Y10-pos.raw SUBJECT_SAMPLE_FACTORS - Y14 Age:2-3 months | Estrus Stage:Diestrus RAW_FILE_NAME=Y14-neg.raw; RAW_FILE_NAME=Y14-pos.raw SUBJECT_SAMPLE_FACTORS - QC1 Age:control | Estrus Stage:control RAW_FILE_NAME=QC1-neg.raw; RAW_FILE_NAME=QC1-pos.raw SUBJECT_SAMPLE_FACTORS - QC2 Age:control | Estrus Stage:control RAW_FILE_NAME=QC2-neg.raw; RAW_FILE_NAME=QC2-pos.raw SUBJECT_SAMPLE_FACTORS - QC3 Age:control | Estrus Stage:control RAW_FILE_NAME=QC3-neg.raw; RAW_FILE_NAME=QC3-pos.raw SUBJECT_SAMPLE_FACTORS - QC4 Age:control | Estrus Stage:control RAW_FILE_NAME=QC4-neg.raw; RAW_FILE_NAME=QC4-pos.raw #COLLECTION CO:COLLECTION_SUMMARY Young (Y; 2-3-month-old) and middle-aged (MA; 9-10-month-old, retired breeders) CO:COLLECTION_SUMMARY female rats (Sprague Dawley, Charles River, Beijing) were fed with CO:COLLECTION_SUMMARY radiation-sterilized lab rodent feed (number 1010086; Jiangsu Xietong CO:COLLECTION_SUMMARY Pharmaceutical Bio-engineering Co., Ltd.) and water ad libitum. A 12-hour CO:COLLECTION_SUMMARY light/12-hour dark cycle (lights on at 8 a.m.) and the room temperature at 23℃ CO:COLLECTION_SUMMARY was held. Estrous periodicity was detected by vaginal smear for at least CO:COLLECTION_SUMMARY consecutive two cycles (ten days). Only rats in possession of two regular CO:COLLECTION_SUMMARY estrous periods (four to five days) were included for the subsequent assays. On CO:COLLECTION_SUMMARY the basis of age and estrous stage, the rats were assigned to one of the CO:COLLECTION_SUMMARY following subgroups respectively: young, proestrus and diestrus (Y-P and Y-D); CO:COLLECTION_SUMMARY middle-aged, proestrus and diestrus (MA-P and MA-D). All fecal specimens were CO:COLLECTION_SUMMARY harvested and quickly chilled in liquid nitrogen and finally transferred to CO:COLLECTION_SUMMARY -80°C refrigerator for subsequent experiments. CO:SAMPLE_TYPE Feces #TREATMENT TR:TREATMENT_SUMMARY Young (Y; 2-3-month-old) and middle-aged (MA; 9-10-month-old, retired breeders) TR:TREATMENT_SUMMARY female rats (Sprague Dawley, Charles River, Beijing) were fed with TR:TREATMENT_SUMMARY radiation-sterilized lab rodent feed (number 1010086; Jiangsu Xietong TR:TREATMENT_SUMMARY Pharmaceutical Bio-engineering Co., Ltd.) and water ad libitum. A 12-hour TR:TREATMENT_SUMMARY light/12-hour dark cycle (lights on at 8 a.m.) and the room temperature at 23℃ TR:TREATMENT_SUMMARY was held. Estrous periodicity was detected by vaginal smear for at least TR:TREATMENT_SUMMARY consecutive two cycles (ten days). Only rats in possession of two regular TR:TREATMENT_SUMMARY estrous periods (four to five days) were included for the subsequent assays. On TR:TREATMENT_SUMMARY the basis of age and estrous stage, the rats were assigned to one of the TR:TREATMENT_SUMMARY following subgroups respectively: young, proestrus and diestrus (Y-P and Y-D); TR:TREATMENT_SUMMARY middle-aged, proestrus and diestrus (MA-P and MA-D). #SAMPLEPREP SP:SAMPLEPREP_SUMMARY The fecal samples weighed 60 mg were transferred to 1.5-mL EP tubes with SP:SAMPLEPREP_SUMMARY addition of 20 μL L-2-chlorophenylalanine (0.3 mg/mL) and 20 μL Lyso PC17:0 SP:SAMPLEPREP_SUMMARY (0.01 mg/ml) in methanol and 600 μL methanol/water, 4:1 (v/v). After pre-cooled SP:SAMPLEPREP_SUMMARY at -20℃ for 2 min, the samples were ground at 60 Hz for 2 min by steel beads, SP:SAMPLEPREP_SUMMARY sonicated for 10 min and centrifuged for 10 min at 13,000 rpm, 4℃ following SP:SAMPLEPREP_SUMMARY standing still at -20℃ for 30 min. 300 μL of supernatants were dried and then SP:SAMPLEPREP_SUMMARY resolved in 400 μL methanol/water, 1:4 (v/v). The mixtures were vortexed for 30 SP:SAMPLEPREP_SUMMARY s, sonicated for 2 min and centrifuged at 13,000 rpm, 4℃ for 10 min. 150 μL SP:SAMPLEPREP_SUMMARY supernatant was aspirated with syringes and filtered through 0.22 μm organic SP:SAMPLEPREP_SUMMARY phase pinhole filters. The extracts were transferred to LC injection vials and SP:SAMPLEPREP_SUMMARY store at -80℃ until LC-MS analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) CH:SOLVENT_A 100% water; 0.1%formic acid CH:SOLVENT_B 100% acetonitrile; 0.1%formic acid CH:FLOW_GRADIENT 0.35 mL/min: 5-20% B, 0-2 min; 20-25% B, 2-4 min; 25-60% B, 4-9 min; 60-100% B, CH:FLOW_GRADIENT 9-14 min; 100% B, 14-16 min; 100-5% B, 16-16.1 min; 5% B, 16.1-18.1 min CH:FLOW_RATE 0.35 mL/min CH:COLUMN_TEMPERATURE 50 #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 NEGATIVE MS:MS_COMMENTS - MS:MS_RESULTS_FILE ST003003_AN004934_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END