Summary of Study ST002753
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 PR001714. The data can be accessed directly via it's Project DOI: 10.21228/M8542K 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 | ST002753 |
| Study Title | Comparative analyses of metabolome for the intact mammary ducts of 8-week-old MMTV-Neu-IRES-Cre mice versus their wildtype littermates |
| Study Type | Comparative |
| Study Summary | Transgenic overexpression of HER2/Neu oncogene in murine mammary glands result in mammary tumor formation. To elucidate the potential changes in the metabolic activities of HER2/Neu-overexpressing mammary epithelia prior to any obvious tumorigenic growth, we isolated intact mammary ducts from the No:4 inguinal mammary glands of 8-week-old MMTV-Neu-IRES-Cre and WT littermate mice via mild collagenase treatment and performed a LC/MS based untargeted metabolomics assay. |
| Institute | Manchester Institute of Biotechnology, University of Manchester |
| Last Name | Ucar |
| First Name | Ahmet |
| Address | Michael Smith building, Oxford Road, Manchester, M13 9PT, UK |
| ahmet.ucar@manchester.ac.uk | |
| Phone | 00447928839333 |
| Submit Date | 2023-06-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-12-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001714 |
| Project DOI: | doi: 10.21228/M8542K |
| Project Title: | Metabolomics of intact murine mammary ducts at a pre-cancerous stage |
| Project Type: | LC/MS |
| Project Summary: | Metabolomics analyses of intact mammary ducts isolated from 8-week-old MMTV-Neu-IRES-Cre mice and their wildtype littermates |
| Institute: | University of Manchester |
| Last Name: | Ucar |
| First Name: | Ahmet |
| Address: | Oxford Road, Manchester, Lancashire, M13 9PT, United Kingdom |
| Email: | ahmet.ucar@manchester.ac.uk |
| Phone: | 00447928839333 |
| Funding Source: | Breast Cancer Now (BCN) |
Subject:
| Subject ID: | SU002860 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 8-week-old |
| Gender: | Female |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA289483 | Blank | Blank |
| SA289484 | 407 668 | MMTV-NIC |
| SA289485 | 407 667 | MMTV-NIC |
| SA289486 | 407 663 | MMTV-NIC |
| SA289487 | 407 662 | MMTV-NIC |
| SA289488 | QC5 | Quality Control |
| SA289489 | QC6 | Quality Control |
| SA289490 | QC4 | Quality Control |
| SA289491 | QC1 | Quality Control |
| SA289492 | QC3 | Quality Control |
| SA289493 | QC2 | Quality Control |
| SA289494 | 407 661 | Wildtype |
| SA289495 | 407 660 | Wildtype |
| SA289496 | 407 669 | Wildtype |
| Showing results 1 to 14 of 14 |
Collection:
| Collection ID: | CO002853 |
| Collection Summary: | Intact mammary ducts were isolated from No:4 glands of 8-week-old mice using a mild collagenase treatment and size selection using a 100 um mesh. |
| Sample Type: | Breast |
Treatment:
| Treatment ID: | TR002869 |
| Treatment Summary: | There was no additional treatment. |
Sample Preparation:
| Sampleprep ID: | SP002866 |
| Sampleprep Summary: | Ductal organoids were centrifuged, tissue pellets were snap-frozen in liquid nitrogen and then resuspended in 50% Methanol to incubate overnight at 4 °C. Next day, samples were centrifuged at 20,000 x g for 3 min and the top 50 µl supernatant was transferred to a glass autosampler vial with 300 µl insert and capped. Quality control samples were made by pooling 10 µl from each sample. |
Chromatography:
| Chromatography ID: | CH003352 |
| Chromatography Summary: | A sample volume of 5 μL was injected by pulled loop onto a 5 μL sample loop with 150 μl post-injection needle wash with 9:1 acetonitrile and water. Injection cycle time was 1 min per sample. Separations were performed using an Agilent Poroshell 120 HILIC-Z column with dimensions of 150 mm length, 2.1 mm diameter and 2.7 μm particle size equipped with a guard column of the same phase. Mobile phase A was water with 10 mM ammonium acetate adjusted to pH 9 with ammonium hydroxide and 20 µM medronic acid, mobile phase B was 85:15 acetonitrile and water with 10 mM ammonium acetate adjusted to pH 9 with ammonium hydroxide and 20 µM medronic acid. Separation was performed by gradient chromatography at a flow rate of 0.25 ml/min, starting at 96 % B for 2 minutes, ramping to 65 % B over 20 min, hold at 65 % B for 2 min, then back to 96 % B. Re-equilibration time was 5 min. Total run time including 1 min injection cycle was 30 min. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Agilent Poroshell 120 HILIC-Z column (150 mm length, 2.1 mm diameter and 2.7 μm particle size) |
| Column Temperature: | 50 |
| Flow Gradient: | starting at 96 % B for 2 minutes, ramping to 65 % B over 20 min, hold at 65 % B for 2 min, then back to 96 % B |
| Flow Rate: | 0.25 ml/min |
| Solvent A: | 100% water; 10 mM ammonium acetate (pH 9); 20 µM medronic acid |
| Solvent B: | 85% acetonitrile/ 15% water; 10 mM ammonium acetate (pH 9); 20 µM medronic acid |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN004467 |
| Analysis Type: | MS |
| Chromatography ID: | CH003352 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST002753_AN004467_Results.txt |
| Units: | Normalized peak area |
