Summary of Study ST002506

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 PR001619. The data can be accessed directly via it's Project DOI: 10.21228/M8F41P This work is supported by NIH grant, U2C- DK119886.

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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 IDST002506
Study TitleNatural abundance of isotopic metabolite detection in mouse eye orgnaoids.
Study SummaryBecause the natural abundance of isotopic metabolites in the early eye organoids has not yet been reported, we have performed LC-MS/MS without exogenous isotopic labeling to show the natural abundance of isotopic carbons. Cell Name AES0145 : Rx-GFP K/I EB5 (RIKEN Cell Bank): Organoid method (PMID: 21475194).
Institute
Northwestern University
Last NameTAKATA
First NameNOZOMU
Address303 East Superior Street, 10-220
Emailnozomu.takata@northwestern.edu
Phone3125036066
Submit Date2023-03-15
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-05-01
Release Version1
NOZOMU TAKATA NOZOMU TAKATA
https://dx.doi.org/10.21228/M8F41P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001619
Project DOI:doi: 10.21228/M8F41P
Project Title:Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis
Project Summary:Mammalian retinal metabolism favors aerobic glycolysis. However, the role of glycolytic metabolism in retinal morphogenesis remains unknown. Here we report that aerobic glycolysis is necessary for the early stages of retinal development. Taking advantage of an unbiased approach that combines the use of eye organoids and single-cell RNA sequencing we identified specific glucose transporters and glycolytic genes in retinal progenitors. Next, we determined that the optic vesicle territory of mouse embryos displays elevated levels of glycolytic activity. At the functional level, we found that removal of Glut1 (also known as Slc2a1) and Lactate dehydrogenase A (Ldha) gene activity from developing retinal progenitors arrested eye morphogenesis. Surprisingly, we uncovered that lactate-mediated upregulation of key eye-field transcription factors was controlled by the epigenetic modification of histone H3 acetylation through histone deacetylase (Hdac) activity. Our results identify a novel bioenergetic independent role of lactate as a signaling molecule necessary for mammalian eye morphogenesis.
Institute:Northwestern University
Last Name:TAKATA
First Name:NOZOMU
Address:303 East Superior Street, 10-220, Chicago, Illinois, 60611, USA
Email:nozomu.takata@northwestern.edu
Phone:13125036066

Subject:

Subject ID:SU002606
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 Treatment
SA252365Natural_abundance3Wild-type Control
SA252366Natural_abundance2Wild-type Control
SA252367Natural_abundance1Wild-type Control
Showing results 1 to 3 of 3

Collection:

Collection ID:CO002599
Collection Summary:Collect embryonic stem cell derived eye organoids without isotopic labeling. Three biologically independent repeated samples were collected.
Collection Protocol Filename:Glucose_and_lactate_isotope_labeling.pdf
Sample Type:Retina

Treatment:

Treatment ID:TR002618
Treatment Summary:No treatment was perfomed.

Sample Preparation:

Sampleprep ID:SP002612
Sampleprep Summary:The eye organoids were collected and washed twice with PBS before pellets were flash-frozen and stored at −80°C until metabolite extraction. Metabolite analysis was performed as described previously (PMID: 33931446). Briefly, for metabolite extraction, 80% methanol was used followed by the rapid freeze-thaw method to break the tissues. The supernatant underwent speedvac drying. The samples were prepared in 80% acetonitrile and were analyzed by High-Resolution Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS).

Combined analysis:

Analysis ID AN004128
Analysis type MS
Chromatography type HILIC
Chromatography system Q-exactive
Column Waters XBridge BEH Amide (100 x 3.0mm, 3.5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units Peak area

Chromatography:

Chromatography ID:CH003058
Instrument Name:Q-exactive
Column Name:Waters XBridge BEH Amide (100 x 3.0mm, 3.5um)
Column Temperature:40
Flow Gradient:0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1-18 min, 75% A; 18-25 min, 15% A with a flow rate of 150 μL/min
Flow Rate:150 μL/mi
Solvent A:95% water/5% acetonitrile; 10 mM ammonium hydroxide; 10 mM ammonium acetate, pH 9.0
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS003875
Analysis ID:AN004128
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The capillary of the ESI source was set to 275 °C, with sheath gas at 35 arbitrary units, auxiliary gas at 5 arbitrary units and the spray voltage at 4.0 kV. In positive/negative polarity switching mode, an m/z scan range from 60 to 900 was chosen and MS1 data was collected at a resolution of 70,000. The automatic gain control (AGC) target was set at 1 × 106 and the maximum injection time was 200 ms. The top 5 precursor ions were subsequently fragmented, in a data-dependent manner, using the higher energy collisional dissociation (HCD) cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. Besides matching m/z, metabolites are identified by matching either retention time with analytical standards and/or MS2 fragmentation pattern. Data acquisition and analysis were carried out by Xcalibur 4.1 software and Tracefinder 4.1 software, respectively (both from Thermo Fisher Scientific)
Ion Mode:UNSPECIFIED
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