Summary of Study ST002705

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 PR001676. The data can be accessed directly via it's Project DOI: 10.21228/M82H8Q 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 IDST002705
Study TitleLipidomic Analysis of subventricular zone in adult mice.
Study SummaryLipid metabolism plays an important role in neurogenesis. The present study was performed to investigate the role of serine racemase in lipid metabolism and adult neurogenesis. Conditional deletion of serine racemase in nestin precursor cells (nestin cre+) showed significant alterations in the different lipid classes in the subventricular zone of adult nestin-cre+ mice based on a lipidomics study. The raw data for the lipidomics study are presented.
Institute
Johns Hopkins University School of Medicine
Last NameRoychaudhuri
First NameRobin
Address655 West Baltimore Street
Emailrobinroychaudhuri@gmail.com
Phone3108484336
Submit Date2023-04-29
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-06-22
Release Version1
Robin Roychaudhuri Robin Roychaudhuri
https://dx.doi.org/10.21228/M82H8Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001676
Project DOI:doi: 10.21228/M82H8Q
Project Title:Lipidomic Analysis of subventricular zone in conditional deletion of serine racemase in adult mice.
Project Summary:Lipid metabolism plays an important role in neurogenesis. The present study was performed to investigate the role of serine racemase in lipid metabolism and adult neurogenesis. Conditional deletion of serine racemase in nestin precursor cells (nestin cre+) showed significant alterations in the different lipid classes in the subventricular zone of adult nestin-cre+ mice based on a lipidomics study. The raw data for the lipidomics study are presented.
Institute:Johns Hopkins University School of Medicine
Department:Neuroscience
Laboratory:Solomon H Snyder
Last Name:Roychaudhuri
First Name:Robin
Address:655 West Baltimore Street, Baltimore, Maryland, 21201, USA
Email:robinroychaudhuri@gmail.com
Phone:310-848-4336

Subject:

Subject ID:SU002810
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA272150Nestin CreP 2-2Nes-Cre+
SA272151Nestin CreP 2-1Nes-Cre+
SA272152Nestin CreP 2-3Nes-Cre+
SA272153Nestin Cre 1-2NNes-Cre+
SA272154Nestin Cre 1-1NNes-Cre+
SA272155Nestin CreP 1-3Nes-Cre+
SA272156Nestin CreP 1-2Nes-Cre+
SA272157Nestin Cre 2-3NNes-Cre+
SA272158Nestin Cre 2-2NNes-Cre+
SA272159Nestin Cre 2-1NNes-Cre+
SA272160Nestin CreP 1-1Nes-Cre+
SA272161Nestin Cre 1-3NNes-Cre+
SA272162SR Flox 2-3NWild type
SA272163SR Flox 2-2NWild type
SA272164SR Flox 1-1NWild type
SA272165SR FloxP 2-1Wild type
SA272166SR FloxP 1-3Wild type
SA272167SR FloxP 1-2Wild type
SA272168SR FloxP 2-2Wild type
SA272169SR FloxP 2-3Wild type
SA272170SR Flox 1-3NWild type
SA272171SR Flox 1-2NWild type
SA272172SR FloxP 1-1Wild type
SA272173SR Flox 2-1NWild type
Showing results 1 to 24 of 24

Collection:

Collection ID:CO002803
Collection Summary:Mouse sub ventricular zone tissue was micro dissected and frozen in liquid nitrogen and stored in -80C till further processing.
Collection Protocol Filename:SVZ_Dissection_Protocol-Roychaudhuri_et_al.pdf
Sample Type:sub ventricular zone tissue

Treatment:

Treatment ID:TR002819
Treatment Summary:No treatment was performed. Nestin -cre+ mice used in the study are conditional knockout for Serine Racemase.
Treatment Protocol Filename:Treatment_Protocol-Roychaudhuri_et_al.pdf

Sample Preparation:

Sampleprep ID:SP002816
Sampleprep Summary:SVZ Tissues were micro dissected according to protocol.
Sampleprep Protocol Filename:SVZ_Dissection_Protocol-Roychaudhuri_et_al.pdf

Combined analysis:

Analysis ID AN004385 AN004386
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um) Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Bruker micrOTOFQ II Bruker micrOTOFQ II
Ion Mode POSITIVE NEGATIVE
Units intensity intensity

Chromatography:

Chromatography ID:CH003290
Methods Filename:MS_Metadata-Roychaudhuri_et_al.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um)
Column Temperature:42
Flow Gradient:25 min gradient separation (0 min – 2% MPB, 250 μL/min; 3.0 min – 5% MPB, 250 μL/min; 8.0 min – 30% MPB, 250 μL/min; 21 min – 95% MPB, 230 μL/min; 25 min – 95% MPB, 230 μL/min); and 10 min re-equilibration (0 min – 95% MPB, 230 μL/min; 2 min – 5% MPB, 250 μL/min; 9.95 min – 5% MPB, 250 μL/min; 10 min – 5% MPB, 50 μL/min).
Flow Rate:250 microliter/min
Solvent A:Nova MT MixA: 10 mM ammonium formate in 50:40:10 methanol/acetonitrile/water
Solvent B:Nova MT MixB: 10 mM ammonium formate in 95:5 isopropanol/water
Chromatography Type:Reversed phase

MS:

MS ID:MS004134
Analysis ID:AN004385
Instrument Name:Bruker micrOTOFQ II
Instrument Type:QTOF
MS Type:ESI
MS Comments:m/z 150-1500 range Lipid features were extracted and aligned using NovaMT LipidScreener.
Ion Mode:POSITIVE
Analysis Protocol File:MS_Metadata-Roychaudhuri_et_al.pdf
  
MS ID:MS004135
Analysis ID:AN004386
Instrument Name:Bruker micrOTOFQ II
Instrument Type:QTOF
MS Type:ESI
MS Comments:m/z 150-1500 range Lipid features were extracted and aligned using NovaMT LipidScreener.
Ion Mode:NEGATIVE
Analysis Protocol File:MS_Metadata-Roychaudhuri_et_al.pdf
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