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.
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| 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. |
Combined analysis:
| Analysis ID | AN004467 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Agilent Poroshell 120 HILIC-Z column (150 mm length, 2.1 mm diameter and 2.7 μm particle size) |
| MS Type | ESI |
| MS instrument type | Triple TOF |
| MS instrument name | ABI Sciex 6600 TripleTOF |
| Ion Mode | NEGATIVE |
| Units | Normalized peak area |
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 |
MS:
| MS ID: | MS004214 |
| Analysis ID: | AN004467 |
| Instrument Name: | ABI Sciex 6600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer ran in negative mode under the following source conditions: curtain gas pressure, 50 psi; ionspray voltage, -4500 V; temperature, 400 °C; ESI nebulizer gas pressure, 50 psi; heater gas pressure, -70 psi; declustering potential, -80 V. Data was acquired in an information dependent manner across 10 high sensitivity product ion scans, each with an accumulation time of 100 ms and a TOF survey scan with accumulation time of 250 ms. Total cycle time was 1.3 s. Collision energy was determined using the formula CE (V) = 0.084 x m/z +12 up to a maximum of 55 V. Isotopes within 4 Da were excluded from the scan. Acquired data were checked in PeakView 2.2 and imported into Progenesis Qi 2.4 for metabolomics, where they were aligned, peaks were picked, normalized to all compounds and deconvoluted according to standard Progenesis workflows. Annotations were made by searching the accurate mass, MS/MS spectrum and isotope distribution ratios of acquired data against the NIST MS/MS metabolite library. Metabolites were identified by searching retention times and accurate masses against an in-house chemical standard library. A validated identification is only given if identical hits are made against both the NIST MS/MS and in-house chemical standard libraries. Samples were grouped according to the mouse genotypes (i.e WT or MMTV-Neu) and were filtered based on the following statistical criteria – a maximum fold change between sample groups of at least 1.5-fold, ANOVA p values of <0.05, minimum CV of <30 % and a minimum normalized abundance of 10. |
| Ion Mode: | NEGATIVE |
