Summary of Study ST003643

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 PR002253. The data can be accessed directly via it's Project DOI: 10.21228/M8DC25 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 IDST003643
Study TitleMetabolite analysis for WT and BnaMYB52 mutants by LC-MS/MS
Study SummaryBnaA09.MYB52 directly targets the BnaBAN promoters and promotes BnaBAN expression in Brassica napus. BAN, encoding anthocyanidin reductase that converts anthocyanidins to 2,3- cis-flavan-3-ols compounds (proanthocyanidins starter units), is involved in the flavonoid biosynthesis pathway. Thus, Metabolite analysis was conducted to detect the content of flavonoid in WT (Wild-type), OE (BnaA09.MYB52 overexpression lines in the genetic background Westar) and mutants (four homologous genes of BnaMYB52 knocked out) plants. About 0.1 g mature seeds were collected from WT, OE and mutant plants. Metabolites analysis demonstrated that BnaMYB52 positively regulated the content of several metabolites (such as L-phenylalanine, p-coumaric acid, grosvenorine and astragalin) in flavonoid pathway.
Institute
Huazhong Agricultural University
Last NameJiang
First NameYe
AddressShi Zishan Street 1th, Wuhan, Hubei, 430070, China
Emailvyejiang@163.com
Phone13697353446
Submit Date2024-12-21
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2025-01-26
Release Version1
Ye Jiang Ye Jiang
https://dx.doi.org/10.21228/M8DC25
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002253
Project DOI:doi: 10.21228/M8DC25
Project Title:Metabolite analysis for WT and BnaMYB52 mutants by LC-MS/MS
Project Type:LC-MS/MS
Project Summary:BnaA09.MYB52 directly targets the BnaBAN promoters and promotes BnaBAN expression in B. napus. BAN, encoding anthocyanidin reductase that converts anthocyanidins to 2,3- cis-flavan-3-ols compounds (proanthocyanidins starter units), is involved in the flavonoid biosynthesis pathway. Thus, Metabolite analysis was conducted to detect the content of flavonoid in WT (Wild-type), OE (BnaA09.MYB52 overexpression lines in the genetic background Westar) and mutants (four homologous genes of BnaMYB52 knocked out) plants. The result showed that the content of several metabolites in flavonoid pathway was reduced in mutants, whereas overexpression lines resulted in the opposite trend compared with WT.
Institute:Huazhong Agricultural University
Last Name:Jiang
First Name:Ye
Address:Shi Zishan Street 1th, Wuhan, Hubei, 430070, China
Email:vyejiang@163.com
Phone:13697353446
Publications:Ye et al. Manipulation of seed coat content for increasing oil content via modulating BnaMYB52 in Brassica napus. Cell reports

Subject:

Subject ID:SU003773
Subject Type:Plant
Subject Species:Brassica napus
Taxonomy ID:3708

Factors:

Subject type: Plant; Subject species: Brassica napus (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Genotype
SA39782952CR-1-4Mature seeds Mutant
SA39783052CR-2-4Mature seeds Mutant
SA39783152CR-2-2Mature seeds Mutant
SA39783252CR-2-1Mature seeds Mutant
SA39783352CR-2-3Mature seeds Mutant
SA39783452CR-1-3Mature seeds Mutant
SA39783552CR-1-2Mature seeds Mutant
SA39783652CR-1-1Mature seeds Mutant
SA39783752OE-1-1Mature seeds OE
SA39783852OE-1-2Mature seeds OE
SA39783952OE-1-3Mature seeds OE
SA39784052OE-1-4Mature seeds OE
SA39784152OE-2-1Mature seeds OE
SA39784252OE-2-2Mature seeds OE
SA39784352OE-2-3Mature seeds OE
SA397844WT-4Mature seeds Wide-type
SA397845WT-2Mature seeds Wide-type
SA397846WT-3Mature seeds Wide-type
SA397847WT-1Mature seeds Wide-type
Showing results 1 to 19 of 19

Collection:

Collection ID:CO003766
Collection Summary:WT, OE and bnamyb52 mutant seeds were harvested in May 2024. The harvested seeds were stored at room temperature. The well-filled seeds were selected for metabolomic analysis. Mature seeds were ground into powder in liquid nitrogen, and 0.1 g of dry powder was weighed.
Sample Type:Seeds

Treatment:

Treatment ID:TR003782
Treatment Summary:WT,OE and Homozygous mutants were grown in the genetically modified field of Huazhong Agricultural University in Wuhan from October 2022 to May 2023 and from October 2023 to May 2024. WT indicates Wide-type. OE indicates BnaA09.MYB52 overexpression lines in the genetic background Westar. Mutant indicates four homologous genes of BnaMYB52 knocked out.

Sample Preparation:

Sampleprep ID:SP003780
Sampleprep Summary:Mature seeds were ground into powder in liquid nitrogen, and 0.1 g of dry powder was weighed. The metabolites were extracted overnight under 4℃ with 1.0 mL 70% methanol (V/V) containing 0.1 mg/l acyclovir (an internal standard). After centrifugation at 10,000 g for 5 min, the supernatant was kept and filtered with a membrane (0.22 μm pore size).
Processing Method:Grind in extraction solution
Processing Storage Conditions:4℃
Extraction Method:Extracted overnight under 4℃ with 1.0 mL 70% methanol (V/V) containing 0.1 mg/l acyclovir (an internal standard). After centrifugation at 10,000 g for 5 min, the supernatant was kept and filtered with a membrane
Extract Storage:-80℃

Combined analysis:

Analysis ID AN005982
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 6500 QTrap
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH004544
Instrument Name:Shimadzu 20AD
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40
Flow Gradient:0-0.5min:5%B，0.5-7.5min:ramp to 95%B，7.5-9min:95%B，9-9.1 min：ramp to 5%B，9.1-10min:5%B
Flow Rate:0.35mL/min
Solvent A:99.9% water/0.1% formic acid
Solvent B:99.9% acetonitrile/0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005695
Analysis ID:AN005982
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Acquisition parameters: A scheduled multiple reaction monitoring method was aplied based on comercial standards, with an MRM detection window of 90 s and a target scan time of 1.5 s. For those appeared within the MRM window and have similar MS2 fragments with designated standards, these metabolites that have different retention time are named as isomers. The acquisition volumn is 2 ul. Peak identification criteria: Compared with commercial standards，with retention time of ±0.2 min. Software used: Analyst 1.7.1 with default criteria.
Ion Mode:POSITIVE
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