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

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.

Study ID	ST001477
Study Title	Lipidomics dataset of PTEN deletion-induced nerve regeneration mouse model
Study Summary	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
Submit Date	2020-08-31
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2020-09-10
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA124833	C14_01	Control
SA124834	C14_03	Control
SA124835	C14_04	Control
SA124836	C07_12	Control
SA124837	C07_11	Control
SA124838	C07_09	Control
SA124839	C07_10	Control
SA124840	C14_06	Control
SA124841	C14_08	Control
SA124842	C14_12	Control
SA124843	C14_02	Control
SA124844	C0_01	Control
SA124845	C14_11	Control
SA124846	C14_10	Control
SA124847	C07_08	Control
SA124848	C14_09	Control
SA124849	C14_07	Control
SA124850	C14_05	Control
SA124851	C0_07	Control
SA124852	C0_08	Control
SA124853	C0_09	Control
SA124854	C0_06	Control
SA124855	C0_05	Control
SA124856	C0_02	Control
SA124857	C07_07	Control
SA124858	C0_04	Control
SA124859	C0_10	Control
SA124860	C0_03	Control
SA124861	C07_04	Control
SA124862	C07_05	Control
SA124863	C0_11	Control
SA124864	C07_03	Control
SA124865	C07_06	Control
SA124866	C0_12	Control
SA124867	C07_01	Control
SA124868	C07_02	Control
SA124869	P14_01	KO
SA124870	P14_03	KO
SA124871	P07_13	KO
SA124872	P14_02	KO
SA124873	P07_11	KO
SA124874	P14_04	KO
SA124875	P07_10	KO
SA124876	P07_12	KO
SA124877	P07_09	KO
SA124878	P14_09	KO
SA124879	P14_11	KO
SA124880	P14_12	KO
SA124881	P07_08	KO
SA124882	P14_10	KO
SA124883	P14_08	KO
SA124884	P14_06	KO
SA124885	P14_07	KO
SA124886	P14_05	KO
SA124887	P0_01	KO
SA124888	P0_07	KO
SA124889	P0_08	KO
SA124890	P0_09	KO
SA124891	P0_06	KO
SA124892	P0_05	KO
SA124893	P0_02	KO
SA124894	P0_03	KO
SA124895	P0_04	KO
SA124896	P0_10	KO
SA124897	P0_11	KO
SA124898	P07_04	KO
SA124899	P07_05	KO
SA124900	P07_06	KO
SA124901	P07_03	KO
SA124902	P07_02	KO
SA124903	P0_12	KO
SA124904	P07_01	KO
SA124905	P07_07	KO

Showing results 1 to 73 of 73

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.

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: