Summary of Study ST001303
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 PR000884. The data can be accessed directly via it's Project DOI: 10.21228/M8DX2P 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 | ST001303 |
| Study Title | TGF-Beta 3 heterozygous mice |
| Study Type | Mice nephropathy in lipotoxic model |
| Study Summary | Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening. |
| Institute | University Rey Juan Carlos |
| Department | Basics Science of Health |
| Last Name | Lanzon |
| First Name | Borja |
| Address | Avenida de Atenas S/N |
| borja.lanzon@urjc.es | |
| Phone | 663692554 |
| Submit Date | 2019-12-19 |
| Num Groups | 2 |
| Total Subjects | 14 |
| Num Males | 14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2020-03-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000884 |
| Project DOI: | doi: 10.21228/M8DX2P |
| Project Title: | TGFβ3 heterozygous mice |
| Project Type: | Mice nephropathy in lipotoxic model |
| Project Summary: | Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening. |
| Institute: | University Rey Juan Carlos |
| Department: | Basics Science of Health |
| Last Name: | Lanzon |
| First Name: | Borja |
| Address: | Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain |
| Email: | borja.lanzon@urjc.es |
| Phone: | 663692554 |
Subject:
| Subject ID: | SU001377 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | c57bl6 |
| Age Or Age Range: | 16 weeks |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA094330 | 98 HZCD | HZCD |
| SA094331 | 269 HZCD | HZCD |
| SA094332 | 127 HZCD | HZCD |
| SA094333 | 25 HZCD | HZCD |
| SA094334 | 119 HZCD | HZCD |
| SA094335 | 130 HZCD | HZCD |
| SA094336 | 267 HZCD | HZCD |
| SA094337 | QC2 | QC |
| SA094338 | QC3 | QC |
| SA094339 | QC5 | QC |
| SA094340 | QC1 | QC |
| SA094341 | QC4 | QC |
| SA094342 | 120 WTCD | WTCD |
| SA094343 | 251 WTCD | WTCD |
| SA094344 | 132 WTCD | WTCD |
| SA094345 | 79 WTCD | WTCD |
| SA094346 | 129 WTCD | WTCD |
| SA094347 | 128 WTCD | WTCD |
| SA094348 | 92 WTCD | WTCD |
| Showing results 1 to 19 of 19 |
Collection:
| Collection ID: | CO001372 |
| Collection Summary: | Kidney samples were powdered with mortar and pestle. Method used for extraction was previously validated for tissue |
| Sample Type: | Kidney |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001392 |
| Treatment Summary: | Kidney homogenate was prepared by adding cold (−20 °C) methanol/water (1:1, v/v), (1:10 tissue/solvent). Tissue disruption was achieved with Tissue- Lyser LT homogenizer (Qiagen, Germany) for metabolite extraction. |
Sample Preparation:
| Sampleprep ID: | SP001385 |
| Sampleprep Summary: | 100 μL of kidney tissue homogenate was vortex-mixed with 320 μL of methanol for 2 min, followed by the addition of 80 μL of MTBE for the extraction of nonpolar compounds. Then, vials were rapidly capped and placed on a shaker for 1 h at room temperature. The extracted samples were centrifuged at 4000g for 20 min at 20 °C. For GC−MS analysis, 300 μL of supernatant was evaporated to dryness (SpeedVac Concentrator System, Thermo Fisher Scientific, Waltham, MA). Methoxymation was then performed with 20 μL of O-methoxyamine hydrochloride (15 mg/mL in pyridine) and vigorously vortex-mixed for 5 min. Vials were then incubated in darkness at room temperature for 16 h. For silylation, 20 μL of BSTFA/TMCS (99:1) was added and vortex-mixed for 5 min, and capped vials were placed in the oven at 70 °C for 1 h. Finally, 100 μL of heptane containing tricosane (20 ppm) as internal standard (IS) was added to each vial prior to injection. For LC−MS analysis, 90 μL of supernatant was transferred to an ultra-high-performance liquid chromatography−mass spectrometry. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH001587 |
| Chromatography Summary: | LC-MS (+) |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Poroshell 120 EC-C8 (100 x 2.1mm,2.5um) |
| Column Temperature: | 60 |
| Flow Gradient: | gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 85% methanol/15% isopropanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001588 |
| Chromatography Summary: | LC-MS (-) |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Poroshell 120 EC-C8 (100 x 2.1mm,2.5um) |
| Column Temperature: | 60 |
| Flow Gradient: | gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 85% methanol/15% isopropanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001589 |
| Chromatography Summary: | GC-MS |
| Instrument Name: | Agilent 7890B |
| Column Name: | Agilent DB5-MS (30m x 0.25mm, 0.25um) |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN002169 |
| Analysis Type: | MS |
| Chromatography ID: | CH001587 |
| Num Factors: | 3 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST001303_AN002169_Results.txt |
| Units: | Area |
| Analysis ID: | AN002170 |
| Analysis Type: | MS |
| Chromatography ID: | CH001588 |
| Num Factors: | 3 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST001303_AN002170_Results.txt |
| Units: | Area |
| Analysis ID: | AN002171 |
| Analysis Type: | MS |
| Chromatography ID: | CH001589 |
| Num Factors: | 3 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST001303_AN002171_Results.txt |
| Units: | Area |
