Summary of Study ST003210

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 PR002001. The data can be accessed directly via it's Project DOI: 10.21228/M8ZJ84 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 IDST003210
Study TitleUntargeted metabolomics analysis on single cells and cell clusters of TNBC cell lines using mass spectrometry
Study SummaryTriple-negative breast cancer (TNBC) is more aggressive than other subtypes of breast cancer， and 40% of TNBC patients undergo recurrence and metastasis after treatments. In the metastasis process, clustered cancer cells (cell clusters) exhibited a higher ability of invasion and metastasis. On the other hand, metabolic reprogramming is closely related to the process of cancer metastasis. To explore the metabolic heterogeneity between single cells and cell clusters, mass spectrometry-based untargeted metabolomic analysis was performed on single cells and cell clusters constructed from two TNBC cell lines (MDA-MB-231 and MDA-MB-453). As a result, metabolic profiling between single cells and cell clusters were explored and metabolites contributing to cell clustering were identified.
Institute
Nanjing Medical University
Last NameWang
First NameZhongcheng
Address101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China
Email1845775254@qq.com
Phone025-86868326
Submit Date2024-04-28
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-05-23
Release Version1
Zhongcheng Wang Zhongcheng Wang
https://dx.doi.org/10.21228/M8ZJ84
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002001
Project DOI:doi: 10.21228/M8ZJ84
Project Title:Untargeted metabolomics analysis on single cells and cell clusters of TNBC cell lines using mass spectrometry
Project Summary:Single cells and cell clusters construcetd from two triple-negative breast cancer cell lines (MDA-MB-231 and MDA-MB-453) were used to screen differential metabolites.
Institute:NanJing Medical University
Department:School of Pharmacy
Last Name:Wang
First Name:Zhongcheng
Address:101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China
Email:1845775254@qq.com
Phone:025-86868326

Subject:

Subject ID:SU003329
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample type
SA351494UM009Blank
SA351495UM010Blank
SA351496UM001Blank
SA351497UM008Blank
SA351498UM012Blank
SA351499UM011Blank
SA351500UM002Blank
SA351501UM007Blank
SA351502UM003Blank
SA351503UM004Blank
SA351504UM006Blank
SA351505UM005Blank
SA351506UM040Cell_cluster
SA351507UM041Cell_cluster
SA351508UM042Cell_cluster
SA351509UM039Cell_cluster
SA351510UM035Cell_cluster
SA351511UM043Cell_cluster
SA351512UM036Cell_cluster
SA351513UM037Cell_cluster
SA351514UM038Cell_cluster
SA351515UM051Cell_cluster
SA351516UM050Cell_cluster
SA351517UM034Cell_cluster
SA351518UM052Cell_cluster
SA351519UM049Cell_cluster
SA351520UM048Cell_cluster
SA351521UM045Cell_cluster
SA351522UM046Cell_cluster
SA351523UM047Cell_cluster
SA351524UM044Cell_cluster
SA351525UM031Cell_cluster
SA351526UM018Cell_cluster
SA351527UM033Cell_cluster
SA351528UM020Cell_cluster
SA351529UM021Cell_cluster
SA351530UM017Cell_cluster
SA351531UM016Cell_cluster
SA351532UM013Cell_cluster
SA351533UM014Cell_cluster
SA351534UM015Cell_cluster
SA351535UM022Cell_cluster
SA351536UM019Cell_cluster
SA351537UM030Cell_cluster
SA351538UM023Cell_cluster
SA351539UM032Cell_cluster
SA351540UM028Cell_cluster
SA351541UM029Cell_cluster
SA351542UM024Cell_cluster
SA351543UM027Cell_cluster
SA351544UM025Cell_cluster
SA351545UM026Cell_cluster
SA351546UM068QCs
SA351547UM067QCs
SA351548UM066QCs
SA351549UM065QCs
SA351550UM064QCs
SA351551UM072QCs
SA351552UM071QCs
SA351553UM070QCs
SA351554UM069QCs
SA351555UM057QCs
SA351556UM056QCs
SA351557UM055QCs
SA351558UM054QCs
SA351559UM063QCs
SA351560UM058QCs
SA351561UM053QCs
SA351562UM062QCs
SA351563UM059QCs
SA351564UM061QCs
SA351565UM060QCs
SA351566UM099Single_cell
SA351567UM102Single_cell
SA351568UM101Single_cell
SA351569UM100Single_cell
SA351570UM097Single_cell
SA351571UM103Single_cell
SA351572UM095Single_cell
SA351573UM096Single_cell
SA351574UM098Single_cell
SA351575UM108Single_cell
SA351576UM110Single_cell
SA351577UM111Single_cell
SA351578UM112Single_cell
SA351579UM109Single_cell
SA351580UM094Single_cell
SA351581UM105Single_cell
SA351582UM106Single_cell
SA351583UM107Single_cell
SA351584UM104Single_cell
SA351585UM088Single_cell
SA351586UM078Single_cell
SA351587UM079Single_cell
SA351588UM080Single_cell
SA351589UM081Single_cell
SA351590UM077Single_cell
SA351591UM076Single_cell
SA351592UM073Single_cell
SA351593UM074Single_cell
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Collection:

Collection ID:CO003322
Collection Summary:Two hours before metabolite extraction, the cell culture medium was replaced with fresh medium. Single cell and cell cluster states were collected and centrifuged at 800 × g for 3 min to remove culture media. Then, the cells were resuspended in 1 mL of precooled PBS (4°C) and transferred into a 1.5 mL eppendorf tube. After removing supernatant by centrifugation at 800 × g for 3 min, the tube containing cell pellet was immediately incubated in liquid nitrogen for 1 min to quench enzyme activity and stop the degradation of metabolites.
Collection Protocol Filename:WZC_Collection_protocol.pdf
Sample Type:Cultured cells

Treatment:

Treatment ID:TR003338
Treatment Summary:MDA-MB-231 cells and MDA-MB-453 were maintained in L-15 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37 °C in a free gas exchange with atmospheric air.

Sample Preparation:

Sampleprep ID:SP003336
Sampleprep Summary:300 μL of H2O was then added to the tube, and the cells were fully lysed by an ultrasonic cell disruptor for 10 min at 4°C. After mixing, 20 μL of suspension was collected for protein quantification and subsequent data normalization. Then, methanol (precooled to −80°C) was added into the tube to make 80% methanol solution (v/v). The tube was vortexed vigorously for 5 min and centrifuged at 14,000 × g for 10 min at 4°C to remove the cell debris. Afterward, the metabolite-containing supernatant was transferred to a new tube on ice. The supernatant was evaporated to dryness in a vacuum concentrator and reconstituted in 100 μL of methanol: H2O (1:1, v/v), which was centrifuged again at 14000 × g for 15 min at 4°C to remove insoluble debris.
Sampleprep Protocol Filename:Sampleprep_protocol.pdf

Chromatography:

Chromatography ID:CH003983
Methods Filename:Chromatography_methods.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um)
Column Temperature:40
Flow Gradient:85% B (0 min) to 85% B (1 min) to 65% B (12 min) to 40% B (12.1 min) to 40% B (15 min) to 85% B (15.1 min) to 85% B (20 min), the flow gradient increases linearly between the time points mentioned.
Flow Rate:0.3 mL/min
Solvent A:100% Water; 25 mM Ammonium acetate; 25 mM Ammonium hydroxide
Solvent B:100% Acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH003984
Methods Filename:Chromatography_methods.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Kinetex C18 (100 x 2.1mm,2.6um)
Column Temperature:40
Flow Gradient:10% B (0 min) to 30% B (1 min) to 95% B (19 min) to 95% B (20 min) to 10% B (20.1 min) to 10% B (23 min), the flow gradient increases linearly between the time points mentioned.
Flow Rate:0.4 mL/min
Solvent A:100% Water; 0.1% Formic acid
Solvent B:100% Acetonitrile; 0.1% Formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005262
Analysis Type:MS
Analysis Protocol File:MS_analysis_protocol.pdf
Chromatography ID:CH003983
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003210_AN005262_Results.txt
Units:Peak area
  
Analysis ID:AN005263
Analysis Type:MS
Analysis Protocol File:MS_analysis_protocol.pdf
Chromatography ID:CH003983
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003210_AN005263_Results.txt
Units:Peak area
  
Analysis ID:AN005264
Analysis Type:MS
Analysis Protocol File:MS_analysis_protocol.pdf
Chromatography ID:CH003984
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003210_AN005264_Results.txt
Units:Peak area
  
Analysis ID:AN005265
Analysis Type:MS
Analysis Protocol File:MS_analysis_protocol.pdf
Chromatography ID:CH003984
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003210_AN005265_Results.txt
Units:Peak area
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