{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001477","ANALYSIS_ID":"AN002453","VERSION":"1","CREATED_ON":"September 1, 2020, 3:10 pm"},

"PROJECT":{"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"},

"STUDY":{"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"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"PTEN loxP/loxP mice"},
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{
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}
],
"COLLECTION":{"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_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."},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Accela 600","COLUMN_NAME":"Thermo Acclaim 120 (150 x 2.1mm, 3um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Xcalibur software. LipidSearch for data processing.","MS_RESULTS_FILE":"ST001477_AN002453_Results.txt UNITS:ug/ug protein Has m/z:No Has RT:No RT units:No RT data"},

"MS_METABOLITE_DATA":{
"Units":"ug/ug protein",

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}

}