Summary of Study ST002214

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 PR001414. The data can be accessed directly via it's Project DOI: 10.21228/M8Z42Q This work is supported by NIH grant, U2C- DK119886.

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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 IDST002214
Study TitleThe effects of PKM2 modulation and hypoxia on the metabolic landscape of Alzheimer patient-derived induced neurons
Study SummaryWe have obtained fibroblast cultures from old adult human non-demented control donors and Alzheimer patients (AD). The fibroblasts were reprogrammed into directly induced neurons (iNs) to serve as an adult-like and age-equivalent model for aging and neurodegeneration. Their response to PKM2 modulation (shikonin 10 µM or PKM2 overexpression) and hypoxia (CoDo treatment) were assessed.
Institute
University of Colorado Denver
Last NameHaines
First NameJulie
Address12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Emailjulie.haines@cuanschutz.edu
Phone3037243339
Submit Date2022-06-24
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-07-25
Release Version1
Julie Haines Julie Haines
https://dx.doi.org/10.21228/M8Z42Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001414
Project DOI:doi: 10.21228/M8Z42Q
Project Title:Metabolic changes in Alzheimer patient-derived induced neurons and the effects of PKM2 modulation and hypoxia on their metabolic landscape
Project Summary:We have obtained fibroblast cultures from old adult human non-demented control donors and Alzheimer patients (AD). The fibroblasts were reprogrammed into directly induced neurons (iNs) to serve as an adult-like and age-equivalent model for aging and neurodegeneration. Metabolomic landscape and glucose flux in control versus AD were assessed. Additionally, their response to PKM2 modulation (shikonin 10 µM or PKM2 overexpression) and hypoxia (CoDo treatment) were assessed.
Institute:University of Colorado Denver
Laboratory:Lab of Angelo D'Alessandro in collaboration with lab of Jerome Mertens (Univ of Innsbruck)
Last Name:Haines
First Name:Julie
Address:12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Email:julie.haines@cuanschutz.edu
Phone:3037243339

Subject:

Subject ID:SU002300
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:50-90 yrs
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Condition Treatment
SA2118688020-CAlzheimer patient DMSO
SA2118693131-CAlzheimer patient DMSO
SA2118703053-CAlzheimer patient DMSO
SA2118712800-CAlzheimer patient DMSO
SA2118722800-SAlzheimer patient Shikonin
SA2118738020-SAlzheimer patient Shikonin
SA2118743053-SAlzheimer patient Shikonin
SA2118753131-SAlzheimer patient Shikonin
SA2118768011-DFOnon-demented control CoDo Treatment
SA2118772785-DFOnon-demented control CoDo Treatment
SA2118782785-Cnon-demented control GFP-overexpression
SA2118792608-Cnon-demented control GFP-overexpression
SA2118808011-Cnon-demented control GFP-overexpression
SA2118812608-OEnon-demented control PKM2-overexpression
SA2118822785-OEnon-demented control PKM2-overexpression
SA2118838011-OEnon-demented control PKM2-overexpression
Showing results 1 to 16 of 16

Collection:

Collection ID:CO002293
Collection Summary:For Metabolome, iNs were flow cytometry-isolated 21 days of conversion. iNs were sorted based on the expression of the PSA-NCAM surface markers using PSA-NCAM-PE (Miltenyi) and re-plated on Geltrex-coated wells. The following day, iNs were treated with 2.5 mM DGlucose-C13 for 6 hours and harvested using Tryple. Supernatant and cell pellets were shock frozen in liquid nitrogen.
Sample Type:Biopsy

Treatment:

Treatment ID:TR002312
Treatment Summary:After two weeks of conversion, cells were treated for 10 days with shikonin (10 µM, ChemCruz) before FACS sorting. Control iNs were FACS-sorted and plated on Geltrex-coated wells before transduction with pLVXTP-EGFP-PKM2 or pLVXTP-EGFP. Around 60 % of all neurons were successfully transduced. Five days after transduction, iNs were harvested for MS-analysis. Alternatively, cells were treated with CoDo for 6 hours before harvest.

Sample Preparation:

Sampleprep ID:SP002306
Sampleprep Summary:Metabolites from frozen cell pellets were extracted at 150,000 cells/mL in cold 5:3:2 MeOH:acetonitrile:water. Samples were vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 min, 10,000 g, 4 degrees C). Supernatants were split into two equal tubes and gently dried using a vacuum concentrator. One set of residues were resuspended in 12 uL of 0.1% formic acid (for positive ion mode). The other set of residues were resuspended in 12 uL of 1 mM ammonium acetate (for negative ion mode).

Combined analysis:

Analysis ID AN003622 AN003623
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE POSITIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002677
Chromatography Summary:Negative C18 cells
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Sample Injection:10 uL
Chromatography Type:Reversed phase
  
Chromatography ID:CH002678
Chromatography Summary:Positive C18 cells
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Sample Injection:10 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS003373
Analysis ID:AN003622
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database.
Ion Mode:NEGATIVE
  
MS ID:MS003374
Analysis ID:AN003623
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database.
Ion Mode:POSITIVE
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