Summary of Study ST002213

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 IDST002213
Study TitleMetabolic changes in Alzheimer patient-derived induced neurons versus non-demented controls
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. Metabolomic landscape and glucose flux in control versus AD 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 Date2022-06-22
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 ┬ÁM 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:SU002299
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:50-90 yrs

Factors:

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

mb_sample_id local_sample_id Condition
SA211832AD7 mediaAlzheimer patient
SA211833AD3 mediaAlzheimer patient
SA211834AD6 mediaAlzheimer patient
SA211835AD2 mediaAlzheimer patient
SA211836AD8 mediaAlzheimer patient
SA211837AD1 mediaAlzheimer patient
SA211838AD10 mediaAlzheimer patient
SA211839AD5 mediaAlzheimer patient
SA211840AD11 mediaAlzheimer patient
SA211841AD3Alzheimer patient
SA211842AD5Alzheimer patient
SA211843AD8Alzheimer patient
SA211844AD2Alzheimer patient
SA211845AD7Alzheimer patient
SA211846AD6Alzheimer patient
SA211847AD10Alzheimer patient
SA211848AD11Alzheimer patient
SA211849AD1Alzheimer patient
SA211859Control7 medianon-demented control
SA211860Control4 medianon-demented control
SA211861Control3 medianon-demented control
SA211862Control8 medianon-demented control
SA211863Control6 medianon-demented control
SA211864Control9 medianon-demented control
SA211865Control2 medianon-demented control
SA211866Control10 medianon-demented control
SA211867Control11 medianon-demented control
SA211850Control2Non-demented control
SA211851Control9Non-demented control
SA211852Control8Non-demented control
SA211853Control3Non-demented control
SA211854Control6Non-demented control
SA211855Control11Non-demented control
SA211856Control10Non-demented control
SA211857Control4Non-demented control
SA211858Control7Non-demented control
Showing results 1 to 36 of 36

Collection:

Collection ID:CO002292
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:TR002311
Treatment Summary:n/a

Sample Preparation:

Sampleprep ID:SP002305
Sampleprep Summary:Metabolites from frozen cell pellets were extracted at 1e6 cells/mL in cold 5:3:2 MeOH:acetonitrile:water. Metabolites from supernatant samples (10 uL) were extracted with 240 uL of the above extraction solution. Samples were vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 min, 10,000 g, 4 degrees C).

Combined analysis:

Analysis ID AN003618 AN003619 AN003620 AN003621
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) Phenomenex kinetex C18 (150 x 2.1mm,1.7um) Phenomenex kinetex C18 (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE POSITIVE NEGATIVE POSITIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH002673
Chromatography Summary:Negative C18 cells
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002674
Chromatography Summary:Positive C18 cells
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002675
Chromatography Summary:Negative C18 media
Instrument Name:Thermo Vanquish
Column Name:Phenomenex kinetex C18 (150 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002676
Chromatography Summary:Positive C18 media
Instrument Name:Thermo Vanquish
Column Name:Phenomenex kinetex C18 (150 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003369
Analysis ID:AN003618
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:MS003370
Analysis ID:AN003619
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
  
MS ID:MS003371
Analysis ID:AN003620
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:MS003372
Analysis ID:AN003621
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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