Summary of Study ST000237
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 PR000190. The data can be accessed directly via it's Project DOI: 10.21228/M8Q30F This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000237 |
| Study Title | Quick Comparison of Serum Metabolites in SD Rats of Different Sex by Untargeted UPLC-TOFMS and In-house Software Platform |
| Study Type | Biomarker Discovery |
| Study Summary | Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. Then a blood sample (3-5ml) was collected from the aorta of the rat under anesthesia and centrifuged to obtain serum. All urine and serum samples were frozen at -80°C prior to analysis. |
| Institute | Beijing Institute of Radiation Medicine |
| Department | Department of Pharmacology and Toxicology |
| Last Name | Liang |
| First Name | Qiande |
| Address | 27 Taiping Road, Beijing, P.R.China |
| liangqiande@yeah.net | |
| Submit Date | 2015-08-09 |
| Num Groups | 2 |
| Total Subjects | 16 |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-09-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000190 |
| Project DOI: | doi: 10.21228/M8Q30F |
| Project Title: | Quick Comparison of Metabolites in Human and Rats of Different Sex by Untargeted UPLC-TOFMS and In-house Software Platform_2 |
| Project Type: | Biomarker Discovery |
| Project Summary: | Metabolite difference between sexes has rarely been observed in global manner. In this study, untargeted UPLC-TOFMS and an in-house software platform were used for quick comparison of sex difference of urinary metabolites in human, and of urinary and serum metabolites in SD rats. In addition, as a convenient opportunity, the species difference of urinary metabolites between human and SD rats were also observed. Human urine samples were collected before breakfast from 14 male and 13 female Chinese post-graduate students, age from 23 to 29, on the morning of sample collection day. Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. Then a blood sample (3-5ml) was collected from the aorta of the rat under anesthesia and centrifuged to obtain serum. All urine and serum samples were frozen at -80°C prior to analysis. The study of sex differences is important for finding the best course of treatment of disease as well as for developing novel targets of therapy. A more complete understanding of the metabolic differences across sex-based subgroups is helpful to improve the mechanistic understanding of sex differences. |
| Institute: | Beijing Institute of Radiation Medicine |
| Department: | Department of Pharmacology and Toxicology |
| Last Name: | Liang |
| First Name: | Qiande |
| Address: | 27 Taiping Road, Beijing, P.R.China |
| Email: | liangqiande@yeah.net |
Subject:
| Subject ID: | SU000257 |
| Subject Type: | Animal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Genotype Strain: | Sprague-Dawley rat |
| Weight Or Weight Range: | 220-250g |
| Gender: | Male/Female |
| Animal Housing: | pathogen-free animal facility |
| Animal Light Cycle: | 12h light/dark cycle |
| Animal Feed: | free access to standard food |
| Animal Water: | free access to water |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Gender |
|---|---|---|
| SA011073 | FemaleRat4 | Female |
| SA011074 | FemaleRat3 | Female |
| SA011075 | FemaleRat2 | Female |
| SA011076 | FemaleRat5 | Female |
| SA011077 | FemaleRat6 | Female |
| SA011078 | FemaleRat8 | Female |
| SA011079 | FemaleRat7 | Female |
| SA011080 | FemaleRat1 | Female |
| SA011081 | MaleRat8 | Male |
| SA011082 | MaleRat3 | Male |
| SA011083 | MaleRat2 | Male |
| SA011084 | MaleRat4 | Male |
| SA011085 | MaleRat5 | Male |
| SA011086 | MaleRat7 | Male |
| SA011087 | MaleRat6 | Male |
| SA011088 | MaleRat1 | Male |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO000247 |
| Collection Summary: | Blood sample (3-5ml) was collected from the aorta of the rat under anesthesia and centrifuged to obtain serum |
| Collection Protocol Filename: | 1_COL_PROT.pdf |
| Sample Type: | Serum |
| Collection Method: | Blood sample (3-5ml) was collected from the aorta of the rat under anesthesia and centrifuged to obtain serum |
| Collection Location: | Lab |
| Collection Frequency: | Once |
| Collection Duration: | About 10~60 seconds |
| Volumeoramount Collected: | 3-5ml |
| Storage Conditions: | -80°C |
| Collection Vials: | 15ml Polypropylene tube |
| Storage Vials: | 1.5ml Eppendorf vial |
| Collection Tube Temp: | Room tempreture |
| Blood Serum Or Plasma: | Serum |
Treatment:
| Treatment ID: | TR000267 |
| Treatment Summary: | On the morning of sample collection day, each rat was deprived of food and put in metabolic cage for 24h urine collection. Then a blood sample (3-5ml) was collected from the aorta of the rat under anesthesia and centrifuged to obtain serum. All urine and serum samples were frozen at -80°C prior to analysis. |
| Treatment: | Intervention |
| Treatment Route: | Stay in metabolic cage for 24h urine collection |
| Animal Anesthesia: | Anesthesia using Pentobarbital Sodium |
| Animal Acclimation Duration: | ?3 days |
| Animal Fasting: | 24h |
| Animal Endp Euthanasia: | Died in anesthesia status |
| Animal Endp Tissue Coll List: | Blood |
| Animal Endp Tissue Proc Method: | Centrifuged to obtain serum |
| Animal Endp Clinical Signs: | Died |
Sample Preparation:
| Sampleprep ID: | SP000261 |
| Sampleprep Summary: | Amygdalin was dissolved in acetonitrile-water(1:1) to form 0.1mg/ml solution. Serum samples were unfrozen at room temperature. 500?l of serum sample was mixed with 20?l Amygdalin solution and 100?l 20% Trichloroacetic acid(TCA) solution. After centrifugation at about 14000rpm and -4?, the supernatant was injected into UPLC-TOF MS system. |
| Sampleprep Protocol Filename: | 2_PRE_PROT.pdf |
| Processing Method: | Precipitation |
| Processing Storage Conditions: | Precipitation at room tempreture; centrifugation at -4? |
| Extraction Method: | Precipitation by TCA |
| Extract Concentration Dilution: | 500?l of serum/620?l |
| Extract Storage: | 4? after centrifugation and during analysis |
| Sample Spiking: | 20?l Amygdalin solution/620?l |
Combined analysis:
| Analysis ID | AN000363 | AN000364 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Waters Synapt-HDMS | Waters Synapt-HDMS |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Height | Peak Height |
Chromatography:
| Chromatography ID: | CH000265 |
| Chromatography Summary: | Untargeted UPLC-TOFMS |
| Methods Filename: | 3_CHR_PROT.pdf |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 24? |
| Flow Gradient: | Isocratic 2% B (01 min), linear gradient from 2% to 5% B (12 min), 5% to 12% B (25 min), 12% to 20% B (510 min), 20% to 30% B (1012 min), 30% to 50% B (1213 min), 50% to 100% B (1315 min), isocratic 100% B for 1min, then back to 2% B in 1 min and isocratic 2% B for 3min before next run |
| Flow Rate: | 0.5 ml/min |
| Injection Temperature: | 24? |
| Internal Standard: | Amygdalin |
| Sample Injection: | 8?L |
| Sampling Cone: | 40V |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 20min |
| Capillary Voltage: | Positive ion mode:3kV; Negative ion mode: 2.9kV |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000309 |
| Analysis ID: | AN000363 |
| Instrument Name: | Waters Synapt-HDMS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3kV |
| Collision Energy: | 6V (trap)/4V (transfer) |
| Collision Gas: | Ar |
| Dry Gas Flow: | 900 L/h |
| Dry Gas Temp: | 450? |
| Ion Source Temperature: | 100? |
| Ionization: | ESI |
| Source Temperature: | 100? |
| Desolvation Gas Flow: | 900 L/h |
| Desolvation Temperature: | 450? |
| Acquisition Parameters File: | Inlet_Method_File_Name:_20100505 _Positive_MS_Mehod_File_Name:_20120221_pos_50-1500 |
| Processing Parameters File: | TR_0-18_50-1500_005_020_YES6_YES.mlm |
| MS ID: | MS000310 |
| Analysis ID: | AN000364 |
| Instrument Name: | Waters Synapt-HDMS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 2.9kV |
| Collision Energy: | 6V (trap)/4V (transfer) |
| Collision Gas: | Ar |
| Dry Gas Flow: | 900 L/h |
| Dry Gas Temp: | 450? |
| Ion Source Temperature: | 100? |
| Ionization: | ESI |
| Source Temperature: | 100? |
| Desolvation Gas Flow: | 900 L/h |
| Desolvation Temperature: | 450? |
| Acquisition Parameters File: | Negative_MS_Mehod_File_Name:_20120221_neg_50-1500 |
| Processing Parameters File: | TR_0-18_50-1500_005_020_YES6_YES.mlm |
