Summary of Study ST001272

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 PR000856. The data can be accessed directly via it's Project DOI: 10.21228/M81T3M This work is supported by NIH grant, U2C- DK119886.

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Study IDST001272
Study TitleGrowth cone memebrane and growth cone particulate lipidomics
Study Typeuntargeted LC-MS/MS lipidomics
Study SummaryWe performed high performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the proteome and lipidome of GC from C57BL/6 mice across five age groups (E18, P0, P3, P6, and P9) from two growth cone fractions: growth cone membrane (GCM) and growth cone particulate (GCP)
Institute
University of Miami
DepartmentOphthalmology, Bascom Palmer Eye Institute
LaboratorySanjoy K. Bhattacharya
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Miami, FL 33136
EmailSBhattacharya@med.miami.edu
Phone305-482-4103
Submit Date2019-10-21
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-01-03
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M81T3M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000856
Project DOI:doi: 10.21228/M81T3M
Project Title:Growth cone Membrane lipidomics and Growth cone particulate at different developmental stages in C57BL/6 mice
Project Type:untargeted LC-MS/MS lipidomics
Project Summary:We performed high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the lipidome of GC from C57BL/6 mice across five age groups (E18, P0, P3, P6, and P9) from two growth cone fractions: growth cone membrane (GCM) and growth cone particulate (GCP). These fractions were generated through established differential centrifugation techniques and lipid extraction. Developmental time points were chosen based upon our understanding of brain development in the murine model. In mice cortex, E18 is characterized by extension or elongation of axons toward targets, while around P0-P3 is when axons start innervating targets and branching occurs. At P6-P7 is when target innervation is generally complete and a subpopulation of cortical neurons undergo developmental cell death. By P9 growth cones have mostly disappeared.
Institute:University of Miami
Department:Ophthalmology, Bascom Palmer Eye Institute
Laboratory:Sanjoy K. Bhattacharya
Last Name:Bhattacharya
First Name:Sanjoy
Address:1638 NW 10th Avenue Miami, FL 33136
Email:SBhattacharya@med.miami.edu
Phone:305-482-4103
Contributors:Jennifer Arcuri

Subject:

Subject ID:SU001342
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Age Or Age Range:E18-P90
Weight Or Weight Range:not measured
Height Or Height Range:not measured
Gender:Pooled
Animal Animal Supplier:The Jackson Laboratory
Animal Housing:standard
Animal Light Cycle:standard 12h
Animal Feed:standard grain-based
Animal Water:standard unlimited
Animal Inclusion Criteria:random

Factors:

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

mb_sample_id local_sample_id Fraction Age
SA092629GCM_E18_3-GCM E18
SA092630GCM_E18_3+GCM E18
SA092631GCM_E18_2+GCM E18
SA092632GCM_E18_4+GCM E18
SA092633GCM_E18_2-GCM E18
SA092634GCM_E18_5+GCM E18
SA092635GCM_E18_6-GCM E18
SA092636GCM_E18_6+GCM E18
SA092637GCM_E18_5-GCM E18
SA092638GCM_E18_1-GCM E18
SA092639GCM_E18_4-GCM E18
SA092640GCM_E18_1+GCM E18
SA092641GCM_P0_4-GCM P0
SA092642GCM_P0_4+GCM P0
SA092643GCM_P0_5+GCM P0
SA092644GCM_P0_5-GCM P0
SA092645GCM_P0_6-GCM P0
SA092646GCM_P0_3-GCM P0
SA092647GCM_P0_6+GCM P0
SA092648GCM_P0_1+GCM P0
SA092649GCM_P0_3+GCM P0
SA092650GCM_P0_1-GCM P0
SA092651GCM_P0_2-GCM P0
SA092652GCM_P0_2+GCM P0
SA092653GCM_P3_4-GCM P3
SA092654GCM_P3_4+GCM P3
SA092655GCM_P3_5-GCM P3
SA092656GCM_P3_3-GCM P3
SA092657GCM_P3_5+GCM P3
SA092658GCM_P3_1-GCM P3
SA092659GCM_P3_6+GCM P3
SA092660GCM_P3_1+GCM P3
SA092661GCM_P3_2+.GCM P3
SA092662GCM_P3_2-GCM P3
SA092663GCM_P3_3+GCM P3
SA092664GCM_P3_6-GCM P3
SA092665GCM_P6_5-GCM P6
SA092666GCM_P6_5+GCM P6
SA092667GCM_P6_6+GCM P6
SA092668GCM_P6_6-GCM P6
SA092669GCM_P6_1-GCM P6
SA092670GCM_P6_4+GCM P6
SA092671GCM_P6_4-GCM P6
SA092672GCM_P6_3-GCM P6
SA092673GCM_P6_1+GCM P6
SA092674GCM_P6_2+GCM P6
SA092675GCM_P6_2-GCM P6
SA092676GCM_P6_3+GCM P6
SA092677GCM_P9_4-GCM P9
SA092678GCM_P9_5+GCM P9
SA092679GCM_P9_5-GCM P9
SA092680GCM_P9_6-GCM P9
SA092681GCM_P9_4+GCM P9
SA092682GCM_P9_6+GCM P9
SA092683GCM_P9_1-GCM P9
SA092684GCM_P9_3-GCM P9
SA092685GCM_P9_1+GCM P9
SA092686GCM_P9_2+GCM P9
SA092687GCM_P9_2-GCM P9
SA092688GCM_P9_3+GCM P9
SA092689GCP_E18_3+GCP E18
SA092690GCP_E18_3-GCP E18
SA092691GCP_E18_2-GCP E18
SA092692GCP_E18_4+GCP E18
SA092693GCP_E18_1-GCP E18
SA092694GCP_E18_2+GCP E18
SA092695GCP_E18_4-GCP E18
SA092696GCP_E18_1+GCP E18
SA092697GCP_E18_6-GCP E18
SA092698GCP_E18_6+GCP E18
SA092699GCP_E18_5+GCP E18
SA092700GCP_E18_5-GCP E18
SA092701GCP_P0_5+GCP P0
SA092702GCP_P0_4-GCP P0
SA092703GCP_P0_6+GCP P0
SA092704GCP_P0_1-GCP P0
SA092705GCP_P0_4+GCP P0
SA092706GCP_P0_6-GCP P0
SA092707GCP_P0_5-GCP P0
SA092708GCP_P0_2+GCP P0
SA092709GCP_P0_3-GCP P0
SA092710GCP_P0_1+GCP P0
SA092711GCP_P0_2-GCP P0
SA092712GCP_P0_3+GCP P0
SA092713GCP_P3_5+GCP P3
SA092714GCP_P3_4-GCP P3
SA092715GCP_P3_6+GCP P3
SA092716GCP_P3_6-GCP P3
SA092717GCP_P3_4+GCP P3
SA092718GCP_P3_5-GCP P3
SA092719GCP_P3_2-GCP P3
SA092720GCP_P3_1+GCP P3
SA092721GCP_P3_1-GCP P3
SA092722GCP_P3_2+GCP P3
SA092723GCP_P3_3-GCP P3
SA092724GCP_P3_3+GCP P3
SA092725GCP_P6_1+GCP P6
SA092726GCP_P6_3+GCP P6
SA092727GCP_P6_5+GCP P6
SA092728GCP_P6_6+GCP P6
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Collection:

Collection ID:CO001336
Collection Summary:Growth cone from C57BL/6 mice across five age groups (E18, P0, P3, P6, and P9) from two growth cone fractions: growth cone membrane (GCM) and growth cone particulate (GCP) were collected. These fractions were generated through established differential centrifugation techniques and lipid extraction from established protocols: 1-Estrada-Bernal, A. et al. Functional complexity of the axonal growth cone: a proteomic analysis. PloS one 7, e31858 (2012). 2-Pfenninger et al 1983 paper (Pfenninger, K. H., Ellis, L., Johnson, M. P., Friedman, L. B. & Somlo, S. Nerve growth cones isolated from fetal rat brain: subcellular fractionation and characterization. Cell 35, 573-584 (1983)
Sample Type:Brain

Treatment:

Treatment ID:TR001357
Treatment Summary:No Treatment

Sample Preparation:

Sampleprep ID:SP001350
Sampleprep Summary:We performed high performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the lipidome of GC from C57BL/6 mice across five age groups (E18, P0, P3, P6, and P9) from two growth cone fractions: growth cone membrane (GCM) and growth cone particulate (GCP).

Combined analysis:

Analysis ID AN002112
Analysis type MS
Chromatography type Reversed phase
Chromatography system Accela 600
Column Thermo Acclaim C30 (150 x 2.1mm,3m)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units main area

Chromatography:

Chromatography ID:CH001544
Instrument Name:Accela 600
Column Name:Thermo Acclaim C30 (150 x 2.1mm,3m)
Chromatography Type:Reversed phase

MS:

MS ID:MS001965
Analysis ID:AN002112
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Samples were ran in positive and negative ion mode
Ion Mode:UNSPECIFIED
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