Summary of study ST001477

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 PR001001. The data can be accessed directly via it's Project DOI: 10.21228/M89H64 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST001477
Study TitleLipidomics dataset of PTEN deletion-induced nerve regeneration mouse model
Study SummaryWe present the lipidome of adult PTENloxP/loxP mice subjected to intravitreal injection of adeno-associated viruses expressing Cre (AAV-Cre) as a model of regeneration. At 4-week-old, PTENloxP/loxP mice were intravitreally-injected with 2-3 μl of either AAV-Cre (KO) or AAV-PLAP (control), and two weeks later optic nerve crush was performed. At indicated time-points after crush (0 days, 7 days, 14 days), mice were euthanized and optic nerves were immediately dissected out, and then flash frozen on dry ice. The Bligh and Dyer method was used for lipid extraction, followed by mass spectrometry lipid profiling with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS). The raw scans were analysed with LipidSearch 4.2 and the statistical analysis was conducted through Metaboanalyst 4.0
Institute
University of Miami
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Emailsbhattacharya@med.miami.edu
Phone305-482-4103
Submit Date2020-08-31
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2020-09-10
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M89H64
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001001
Project DOI:doi: 10.21228/M89H64
Project Title:Lipidomics dataset of PTEN deletion-induced nerve regeneration mouse model
Project Summary:The optic nerve is part of the mammalian adult central nervous system (CNS) and has limited capability to regenerate after injury. Deletion of Phosphatase and tensin homolog (PTEN), a negative regulator of the PI3 kinase/Akt pathway, has been shown to promote regeneration in retinal ganglion cells (RGCs) after nerve damage[1, 2]. We present the lipidome of adult PTENloxP/loxP mice subjected to intravitreal injection of adeno-associated viruses expressing Cre (AAV-Cre) as a model of regeneration. At 4-week-old, PTENloxP/loxP mice were intravitreally-injected with 2-3 μl of either AAV-Cre (KO) or AAV-PLAP (control), and two weeks later optic nerve crush was performed. At indicated time-points after crush (0 days, 7 days, 14 days), mice were euthanized and optic nerves were immediately dissected out, and then flash frozen on dry ice. The Bligh and Dyer method was used for lipid extraction, followed by mass spectrometry lipid profiling with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS). The raw scans were analysed with LipidSearch 4.2 and the statistical analysis was conducted through Metaboanalyst 4.0.
Institute:University of Miami
Last Name:Bhattacharya
First Name:Sanjoy
Address:1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Email:sbhattacharya@med.miami.edu
Phone:305-482-4103

Subject:

Subject ID:SU001551
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:PTEN loxP/loxP mice

Factors:

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

mb_sample_id local_sample_id Factor
SA124833C14_01Control
SA124834C14_03Control
SA124835C14_04Control
SA124836C07_12Control
SA124837C07_11Control
SA124838C07_09Control
SA124839C07_10Control
SA124840C14_06Control
SA124841C14_08Control
SA124842C14_12Control
SA124843C14_02Control
SA124844C0_01Control
SA124845C14_11Control
SA124846C14_10Control
SA124847C07_08Control
SA124848C14_09Control
SA124849C14_07Control
SA124850C14_05Control
SA124851C0_07Control
SA124852C0_08Control
SA124853C0_09Control
SA124854C0_06Control
SA124855C0_05Control
SA124856C0_02Control
SA124857C07_07Control
SA124858C0_04Control
SA124859C0_10Control
SA124860C0_03Control
SA124861C07_04Control
SA124862C07_05Control
SA124863C0_11Control
SA124864C07_03Control
SA124865C07_06Control
SA124866C0_12Control
SA124867C07_01Control
SA124868C07_02Control
SA124869P14_01KO
SA124870P14_03KO
SA124871P07_13KO
SA124872P14_02KO
SA124873P07_11KO
SA124874P14_04KO
SA124875P07_10KO
SA124876P07_12KO
SA124877P07_09KO
SA124878P14_09KO
SA124879P14_11KO
SA124880P14_12KO
SA124881P07_08KO
SA124882P14_10KO
SA124883P14_08KO
SA124884P14_06KO
SA124885P14_07KO
SA124886P14_05KO
SA124887P0_01KO
SA124888P0_07KO
SA124889P0_08KO
SA124890P0_09KO
SA124891P0_06KO
SA124892P0_05KO
SA124893P0_02KO
SA124894P0_03KO
SA124895P0_04KO
SA124896P0_10KO
SA124897P0_11KO
SA124898P07_04KO
SA124899P07_05KO
SA124900P07_06KO
SA124901P07_03KO
SA124902P07_02KO
SA124903P0_12KO
SA124904P07_01KO
SA124905P07_07KO
Showing results 1 to 73 of 73

Collection:

Collection ID:CO001546
Collection Summary:All surgical procedures were performed in compliance with animal protocols approved by the IACUC at Boston Children's Hospital. Mice were anaesthetized with ketamine and xylazine and received buprenorphine as a postoperative analgesic. For AAV injection, 4-week-old PtenloxP/loxP mice were intravitreally-injected with 2-3 μl of either AAV-Cre (KO) or AAV-PLAP (control) with a pulled glass micropipette attached to a Hamilton syringe (Hamilton). For intravitreal injections, the pulled-glass micropipette was inserted near the peripheral retina behind the ora serrata and deliberately angled to avoid damage to the lens. Optic nerve crush (ONC) injury was performed two weeks after AAV injection, as per previously described (Park et al., 2008). Briefly, the optic nerve was exposed intraorbitally and crushed with a fine forceps (Dumont #5 FST) for 5 s approximately 500 mm behind the optic disc. Eye ointment was applied post-operatively to protect the cornea. At indicated time-points, mice were euthanized and optic nerves were immediately dissected out, and then flash frozen on dry ice.
Sample Type:Eye tissue

Treatment:

Treatment ID:TR001566
Treatment Summary:adult PTENloxP/loxP mice subjected to intravitreal injection of adeno-associated viruses expressing Cre (AAV-Cre) as a model of regeneration. At 4-week-old, PTENloxP/loxP mice were intravitreally-injected with 2-3 μl of either AAV-Cre (KO) or AAV-PLAP (control), and two weeks later optic nerve crush was performed. At indicated time-points after crush (0 days, 7 days, 14 days), mice were euthanized and optic nerves were immediately dissected out, and then flash frozen on dry ice. The Bligh and Dyer method was used for lipid extraction, followed by mass spectrometry lipid profiling with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS). The raw scans were analysed with LipidSearch 4.2 and the statistical analysis was conducted through Metaboanalyst 4.0.

Sample Preparation:

Sampleprep ID:SP001559
Sampleprep Summary:Lipids were extracted using chloroform, methanol and water mixture to obtain phase separation. Next we performed untargeted liquid chromatography Q-Exactive Orbitrap tandem mass spectrometry (LC-MS/MS) for lipid profiling. We then performed peak extraction, identification, relative quantification, and alignment using Lipid Search 4.2 software.

Combined analysis:

Analysis ID AN002453
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Accela 600
Column Thermo Acclaim 120 (150 x 2.1mm, 3um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units ug/ug protein

Chromatography:

Chromatography ID:CH001797
Instrument Name:Thermo Accela 600
Column Name:Thermo Acclaim 120 (150 x 2.1mm, 3um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002274
Analysis ID:AN002453
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Xcalibur software. LipidSearch for data processing.
Ion Mode:POSITIVE
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