Summary of Study ST002327

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 PR001491. The data can be accessed directly via it's Project DOI: 10.21228/M80M7R 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 IDST002327
Study TitleEffect of PARK7 gene KO on midbrain organoids
Study SummaryDJ1 KO was generated in BJsips iPSC and differentiated into midbrain organoids with the respective iPSC controls. The midbrain organoids were collected at day 40, 100 and 200 after differentiation.
Institute
Icahn School of Medicine at Mount Sinai
Last NameMorrone Parfitt
First NameGustavo
AddressOne Gustave L. Levy Place, Box 1065
Emailgustavo.parfitt@mssm.edu
Phone212-659-5993
Submit Date2022-09-06
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2022-11-18
Release Version1
Gustavo Morrone Parfitt Gustavo Morrone Parfitt
https://dx.doi.org/10.21228/M80M7R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001491
Project DOI:doi: 10.21228/M80M7R
Project Title:DJ1 KO effect on midbrain organoids
Project Summary:DJ1/PARK7 KO human iPSCs and corresponding isogenic controls were differentiated into midbrain organoids. The organoids were collected in different timepoints and submitted to LC-MS/MS for hybrid metabolomics analysis. The objective was to track alterations in glycolysis-related metabolites in different timepoints in the PARK7/DJ1 KO mutation.
Institute:Icahn School of Medicine at Mount Sinai
Last Name:Morrone Parfitt
First Name:Gustavo
Address:1 Gustave L. Levy Pl,, New York, NY, 10029, USA
Email:gustavo.parfitt@mssm.edu
Phone:212-659-5993

Subject:

Subject ID:SU002414
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Group
SA229451Blank 11Blank
SA229452Blank 22Blank
SA229453Blank 7Blank
SA229454Blank 33Blank
SA229455Blank 8Blank
SA229456Blank 9Blank
SA229457Blank 44Blank
SA229458Blank 88Blank
SA229459Blank 77Blank
SA229460Blank 66Blank
SA229461Blank 55Blank
SA229462Blank 10Blank
SA229463Blank 11_1Blank
SA229464Blank 3Blank
SA229465Blank 4Blank
SA229466Blank 5Blank
SA229467Blank 6Blank
SA229468Blank 1Blank
SA229469Blank 2Blank
SA229470Blank 12Blank
SA229471CTR 100 2CTR day 100
SA229472CTR 100 1CTR day 100
SA229473CTR 100 3CTR day 100
SA229474CTR day 200 3CTR day 200
SA229475CTR day 200 5CTR day 200
SA229476CTR day 200 7CTR day 200
SA229477CTR day 200 6CTR day 200
SA229478CTR day 200 4CTR day 200
SA229479CTR day 200 2CTR day 200
SA229480CTR day 200 1CTR day 200
SA229481CTR 40 3CTR day 40
SA229482CTR 40 2CTR day 40
SA229483CTR 40 1CTR day 40
SA229484CTR 40 5CTR day 40
SA229485CTR 40 4CTR day 40
SA229486CTR 40 6CTR day 40
SA229487ISTD 3ISTD
SA229488ISTD 1ISTD
SA229489ISTD 2ISTD
SA229490KO 100 4KO day 100
SA229491KO 100 2KO day 100
SA229492KO 100 5KO day 100
SA229493KO 100 3KO day 100
SA229494KO 100 1KO day 100
SA229495KO day 200 1KO day 200
SA229496KO day 200 8KO day 200
SA229497KO day 200 7KO day 200
SA229498KO day 200 5KO day 200
SA229499KO day 200 4KO day 200
SA229500KO day 200 3KO day 200
SA229501KO day 200 2KO day 200
SA229502KO day 200 6KO day 200
SA229503KO 40 5KO day 40
SA229504KO 40 6KO day 40
SA229505KO 40 4KO day 40
SA229506KO 40 1KO day 40
SA229507KO 40 2KO day 40
SA229508KO 40 3KO day 40
Showing results 1 to 58 of 58

Collection:

Collection ID:CO002407
Collection Summary:Midbrain organoids of day 40, 100 and 200 had a media change 2h prior collection. 5 organoids spheres were added to 1.5 ml tubes and washed in cold PBS twice. The tubes were them frozen in liquid nitrogen.
Collection Protocol Filename:metabolomics_methods.pdf
Sample Type:Brain

Treatment:

Treatment ID:TR002426
Treatment Summary:Organoids bearing PARK7/DJ1 KO mutation were used together with isogenic CTR cell lines (BJSIPS)

Sample Preparation:

Sampleprep ID:SP002420
Sampleprep Summary:After colection,the organoids were extracted in 1 mL/well of 80:20 (v/v) methanol:water with 0.01 ng/mL Val-d8 and Phe-d8 internal extraction standards. extraction solvent was dried under nitrogen gas and metabolite samples were stored at −80 °C until analysis.
Sampleprep Protocol Filename:metabolomics_methods.pdf

Combined analysis:

Analysis ID AN003796
Analysis type MS
Chromatography type HILIC
Chromatography system Dionex Ultimate 3000TM
Column Millipore(TM) ZIC-pHILIC
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE
Units intensity

Chromatography:

Chromatography ID:CH002809
Chromatography Summary:The LC column was a Millipore TMZIC-pHILIC (2.1x150 mm, 5μm) coupled to a Dionex Ultimate 3000TM system and the column oven temperature was set to 25oC for the gradient elution. A flow rate of 100μL/min was used with the 10 mM ammonium carbonate in water (A), pH 9.0, and acetonitrile (B). The gradient profile was 80-20% B (0-30min), 20-80% B (30-31min), 80-80% B (31-42min). Injection volume was set to 2 μL for all analyses (42min total run time per injection).
Methods Filename:metabolomics_methods.pdf
Instrument Name:Dionex Ultimate 3000TM
Column Name:Millipore(TM) ZIC-pHILIC
Column Temperature:25
Flow Gradient:80-20% B (0-30min), 20-80% B (30-31min), 80-80% B (31-42min).
Flow Rate:100µL/min
Solvent A:100% water; 10 mM ammonium carbonate, pH 9.0
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS003538
Analysis ID:AN003796
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Method duration was 30 min with polarity switching data-dependent Top 5method for both positive and negative modes. Spray voltage for both positive and negative modes was 3.5kV and the capillary temperature was set to 320 ⁰C with a sheath gas rate of 35, aux gas of 10, and max spray current of 100 μA. The full MS scan for both polarities utilized 120,000 resolution with an AGC target of 3e6 and a maximum IT of 100 ms, and the scan range was from 67-1000 m/z. Tandem MS spectra for both positive and negative modes used a resolution of 15,000, AGC target of 1 e5, maximum IT of 50 ms, isolation window of 0.4 m/z, isolation offset of 0.1 m/z, fixed first mass of 50 m/z, and 3-way multiplexed normalized collision energies (nCE) of 10, 35, 80. The minimum AGC target was 1e4 with an intensity threshold of 2e5. All data were acquired in profile mode.
Ion Mode:POSITIVE
Analysis Protocol File:metabolomics_methods.pdf
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