Summary of Study ST003003
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001872. The data can be accessed directly via it's Project DOI: 10.21228/M8R41G This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003003 |
| Study Title | Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging |
| Study Summary | Neuroendocrine alterations in the mid-life hypothalamus coupled with reproductive decline herald the initiation of menopausal transition. The certain feature and contribution of gut microflora and metabolites to neuroendocrine changes in the menopausal transition remain largely unknown. Fecal samples of rats experiencing different reproductive stages were collected and processed for 16S rRNA and liquid chromatography-mass spectrometry sequencing. The differences of gut microbiota and metabolites between young and middle-aged rats during proestrus and diestrus were analyzed and their relationships to neuroendocrine aging were then examined. This study documents specific gut microbial composition changes and concomitant shifting trends of metabolites during menopausal transition, which may initiate the gut-brain dysfunction in neuroendocrine aging. |
| Institute | Fudan University |
| Last Name | Dai |
| First Name | Ruoxi |
| Address | 128 Shenyang Road |
| rqdai21@m.fudan.edu.cn | |
| Phone | +86-21-33189900 |
| Submit Date | 2023-12-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-12-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001872 |
| Project DOI: | doi: 10.21228/M8R41G |
| Project Title: | Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging |
| Project Summary: | Neuroendocrine alterations in the mid-life hypothalamus coupled with reproductive decline herald the initiation of menopausal transition. The certain feature and contribution of gut microflora and metabolites to neuroendocrine changes in the menopausal transition remain largely unknown. Fecal samples of rats experiencing different reproductive stages were collected and processed for 16S rRNA and liquid chromatography-mass spectrometry sequencing. The differences of gut microbiota and metabolites between young and middle-aged rats during proestrus and diestrus were analyzed and their relationships to neuroendocrine aging were then examined. This study documents specific gut microbial composition changes and concomitant shifting trends of metabolites during menopausal transition, which may initiate the gut-brain dysfunction in neuroendocrine aging. |
| Institute: | Fudan University |
| Last Name: | Dai |
| First Name: | Ruoxi |
| Address: | 128 Shenyang Road |
| Email: | rqdai21@m.fudan.edu.cn |
| Phone: | +86-21-33189900 |
Subject:
| Subject ID: | SU003117 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Age | Estrus Stage |
|---|---|---|---|
| SA326814 | Y3 | 2-3 months | Diestrus |
| SA326815 | Y1 | 2-3 months | Diestrus |
| SA326816 | Y6 | 2-3 months | Diestrus |
| SA326817 | Y4 | 2-3 months | Diestrus |
| SA326818 | Y10 | 2-3 months | Diestrus |
| SA326819 | Y14 | 2-3 months | Diestrus |
| SA326820 | Y13 | 2-3 months | Proestrus |
| SA326821 | Y5 | 2-3 months | Proestrus |
| SA326822 | Y8 | 2-3 months | Proestrus |
| SA326823 | Y7 | 2-3 months | Proestrus |
| SA326824 | Y9 | 2-3 months | Proestrus |
| SA326825 | MA5 | 9-10 months | Diestrus |
| SA326826 | MA21 | 9-10 months | Diestrus |
| SA326827 | MA25 | 9-10 months | Diestrus |
| SA326828 | MA28 | 9-10 months | Diestrus |
| SA326829 | MA17 | 9-10 months | Diestrus |
| SA326830 | MA4 | 9-10 months | Proestrus |
| SA326831 | MA6 | 9-10 months | Proestrus |
| SA326832 | MA7 | 9-10 months | Proestrus |
| SA326833 | MA26 | 9-10 months | Proestrus |
| SA326834 | MA13 | 9-10 months | Proestrus |
| SA326835 | MA1 | 9-10 months | Proestrus |
| SA326836 | MA34 | 9-10 months | Proestrus |
| SA326837 | QC4 | control | control |
| SA326838 | QC2 | control | control |
| SA326839 | QC1 | control | control |
| SA326840 | QC3 | control | control |
| Showing results 1 to 27 of 27 |
Collection:
| Collection ID: | CO003110 |
| Collection Summary: | Young (Y; 2-3-month-old) and middle-aged (MA; 9-10-month-old, retired breeders) female rats (Sprague Dawley, Charles River, Beijing) were fed with radiation-sterilized lab rodent feed (number 1010086; Jiangsu Xietong Pharmaceutical Bio-engineering Co., Ltd.) and water ad libitum. A 12-hour light/12-hour dark cycle (lights on at 8 a.m.) and the room temperature at 23℃ was held. Estrous periodicity was detected by vaginal smear for at least consecutive two cycles (ten days). Only rats in possession of two regular estrous periods (four to five days) were included for the subsequent assays. On the basis of age and estrous stage, the rats were assigned to one of the following subgroups respectively: young, proestrus and diestrus (Y-P and Y-D); middle-aged, proestrus and diestrus (MA-P and MA-D). All fecal specimens were harvested and quickly chilled in liquid nitrogen and finally transferred to -80°C refrigerator for subsequent experiments. |
| Sample Type: | Feces |
Treatment:
| Treatment ID: | TR003126 |
| Treatment Summary: | Young (Y; 2-3-month-old) and middle-aged (MA; 9-10-month-old, retired breeders) female rats (Sprague Dawley, Charles River, Beijing) were fed with radiation-sterilized lab rodent feed (number 1010086; Jiangsu Xietong Pharmaceutical Bio-engineering Co., Ltd.) and water ad libitum. A 12-hour light/12-hour dark cycle (lights on at 8 a.m.) and the room temperature at 23℃ was held. Estrous periodicity was detected by vaginal smear for at least consecutive two cycles (ten days). Only rats in possession of two regular estrous periods (four to five days) were included for the subsequent assays. On the basis of age and estrous stage, the rats were assigned to one of the following subgroups respectively: young, proestrus and diestrus (Y-P and Y-D); middle-aged, proestrus and diestrus (MA-P and MA-D). |
Sample Preparation:
| Sampleprep ID: | SP003123 |
| Sampleprep Summary: | The fecal samples weighed 60 mg were transferred to 1.5-mL EP tubes with addition of 20 μL L-2-chlorophenylalanine (0.3 mg/mL) and 20 μL Lyso PC17:0 (0.01 mg/ml) in methanol and 600 μL methanol/water, 4:1 (v/v). After pre-cooled at -20℃ for 2 min, the samples were ground at 60 Hz for 2 min by steel beads, sonicated for 10 min and centrifuged for 10 min at 13,000 rpm, 4℃ following standing still at -20℃ for 30 min. 300 μL of supernatants were dried and then resolved in 400 μL methanol/water, 1:4 (v/v). The mixtures were vortexed for 30 s, sonicated for 2 min and centrifuged at 13,000 rpm, 4℃ for 10 min. 150 μL supernatant was aspirated with syringes and filtered through 0.22 μm organic phase pinhole filters. The extracts were transferred to LC injection vials and store at -80℃ until LC-MS analysis. |
Combined analysis:
| Analysis ID | AN004933 | AN004934 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH003723 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 50 |
| 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, 9-14 min; 100% B, 14-16 min; 100-5% B, 16-16.1 min; 5% B, 16.1-18.1 min |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1%formic acid |
| Solvent B: | 100% acetonitrile; 0.1%formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004676 |
| Analysis ID: | AN004933 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | - |
| Ion Mode: | POSITIVE |
| MS ID: | MS004677 |
| Analysis ID: | AN004934 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | - |
| Ion Mode: | NEGATIVE |
