Summary of Study ST001194

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 PR000806. The data can be accessed directly via it's Project DOI: 10.21228/M8H390 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 IDST001194
Study TitleFlavonoid study of Ginkgo leaves facing to different elevation and plant age
Study SummaryGinkgo biloba leaves are always resources for flavonoids pharmaceutical industry. Thus, artificial planting and industrial harvesting become the vital aspect to get higher drug yields. In this research, we performed de novo transcriptome sequencing of Ginkgo leaves coupled with high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry analyses to obtain a comprehensive understanding of the influence of elevation and plant age on flavonoid synthesis. A total of 557,659,530 clean reads were assembled into 188,155 unigenes, of which 135,102 (71.80%) were successfully annotated in seven public databases. The differentially expressed genes analysis indicated DFR, LAR and ANR were significantly up-regulated with the increase of elevation in young Ginkgo trees leaves. With less strict saliency, the relative concentration of flavonoid derivatives with high parent ion signal intensity was likely to support this conclusion. Complex gene variations were observed with the plant age change. However, flavonoid derivatives analysis predicted the potential possibility that the rise of plant age is more likely to be detrimental to the biosynthesis of Ginkgo flavonoids in leaves. From the overall DEGs involved in flavonoid biosynthesis, DFRs seemed to show more considerable variability towards the variation of elevation and plant age. Furthermore, our research effectively expanded the functional genomic library of Ginkgo and provided a reference for artificial planting and industrial harvesting.
Institute
Central South University, China
Last NameZou
First NameKai
AddressCentral South University, 932 Lushan South Road, Yuelu District, Changsha City, Hunan Province
Emailzoukai3412085@hotmail.com
Phone+8615273119784
Submit Date2019-05-05
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2019-07-05
Release Version1
Kai Zou Kai Zou
https://dx.doi.org/10.21228/M8H390
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000806
Project DOI:doi: 10.21228/M8H390
Project Title:Flavonoid study of Ginkgo leaves facing to different elevation and plant age
Project Type:MS quantitative analysis
Project Summary:Flavonoid study of Ginkgo leaves facing to different elevation and plant age
Institute:Central South University, China
Department:School of Minerals Processing and Bioengineering
Laboratory:Key Laboratory of the Ministry of Education
Last Name:Zou
First Name:Kai
Address:Central South University, 932 Lushan South Road, Yuelu District, Changsha City, Hunan Province
Email:zoukai3412085@hotmail.com
Phone:+8615273119784

Subject:

Subject ID:SU001261
Subject Type:Plant
Subject Species:Ginkgo Biloba
Taxonomy ID:3311

Factors:

Subject type: Plant; Subject species: Ginkgo Biloba (Factor headings shown in green)

mb_sample_id local_sample_id Elevation Relative Age
SA083085HO-2High Old
SA083086HO-1High Old
SA083087HO-3High Old
SA083088HY-3High Young
SA083089HY-1High Young
SA083090HY-2High Young
SA083091LO-3Low Old
SA083092LO-1Low Old
SA083093LO-2Low Old
SA083094LY-2Low Young
SA083095LY-1Low Young
SA083096LY-3Low Young
Showing results 1 to 12 of 12

Collection:

Collection ID:CO001255
Collection Summary:The Ginkgo plants grow wildly in Pot bottles of mountain Nature Reserve in Hunan Province, China. A total of twelve trees (26°55'13'' N to 30°6'44'' N, 110°36'16'' E to 110°49'2'' E) were chosen to collect mature leaf samples.
Sample Type:Plant

Treatment:

Treatment ID:TR001276
Treatment Summary:All samples were divided into four groups – low elevation and young age (LY), high elevation and young age (HY), low elevation and older age (LO), high elevation and older age (HO). Each group involved three tree individuals. Each sample was mixed by three copies of ten similarly sized and healthy leaves, which were cut off from the sunny side five meters above the ground of the same tree. After harvesting and short-time surface cleaning by 75% ethanol and sterile water, these leaves were frozen in liquid nitrogen immediately until used.

Sample Preparation:

Sampleprep ID:SP001269
Sampleprep Summary:Andrographolide was dissolved in acetonitrile as an internal standard solution with the terminal concentration of 133μM. Of each leaf sample, 200mg liquid nitrogen-grinded powder was homogenized in 30ml 70% ethanol solution (v: v= 70: 30) followed by 1 min vortex and 1 h ultrasound extraction as previously described with minor modifications (Yu, Lai et al. 2003, Tohge, Nishiyama et al. 2005, Zhou, Yao et al. 2014). After a 13000rpm centrifugation for 10min at 4℃, 1ml supernatant of the solution was transferred and evaporated to dryness under nitrogen gas at 37℃ (Li, Guo et al. 2017). The residue was re-dissolved in 1ml acetonitrile and centrifuged at 13000rpm for 10 min at 4℃. 950μL supernatant was transferred to mix with 50μL internal standard solution to be the final sample for further UPLC-QTOF/MS analysis.
Processing Storage Conditions:Described in summary

Combined analysis:

Analysis ID AN001990
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu LC-30AD Series UPLC system
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type ESI
MS instrument type Triple TOF
MS instrument name ABI Sciex 5600+ TripleTOF
Ion Mode NEGATIVE
Units Peak area

Chromatography:

Chromatography ID:CH001438
Chromatography Summary:Chromatographic separation was completed on a Shimadzu LC-30AD Series UHPLC system (Shimadzu, Duisburg, Germany) equipped with supplementary SIL-30AC injector and (PAD) SPD-M20A detector. ACQUITY UPLCTM BEH C18 column (100 mm × 2.1 mm, 1.7 μm, Waters, Milford, USA) was attached to the whole analyses at 35℃. A flow rate of 0.3 mL/min was chosen to use while 0.1% formic acid water (A) and acetonitrile (B) comprising the mobile phase. The gradient elution conditions were optimized as follows:0-3 min, 5% B → 5% B; 3-25 min, 5% B → 95% B; 25-28 min, 95% B → 95% B; 28-28.1 min, 95% → 5% B, followed by 4 min re-equilibration.
Instrument Name:Shimadzu LC-30AD Series UPLC system
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:35
Flow Gradient:0-3 min, 5% B - 5% B; 3-25 min, 5% B - 95% B; 25-28 min, 95% B - 95% B; 28-28.1 min, 95% - 5% B, followed by 4 min re-equilibration.
Flow Rate:0.3ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS001843
Analysis ID:AN001990
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
MS Comments:AB SCIEX TripleTOF 5600+ system (AB SCIEX Technologies, USA), equipped with electrospray ionization (ESI) source, was coupled to the UHPLC system and used to scan parent ion molecular weight from 100 to 1500. Other MS parameters were set as below: electrospray ionization temperature (℃): 500 (ESI-); nebulizer gas pressure (psi): 60 (ESI-); ion spray voltage (KV): 4.5 (ESI-); collision energies (V): 35 (ESI-). The raw data outputted from LC-MS was pretreated by MarkerView (version 1.2.1.1, AB SCIEX Technologies, USA), including peak recognition (retention time 2 – 28 min, noise threshold 100), alignment, calibration of the internal standard, filtering and normalization to total area. A three-dimensional data set contained sample information, peak retention time (RT), peak relative intensities and mass-to-charge ratio (m/z) was obtained to perform a series of statistical analysis. PeakView (version 1.2.0.3, AB SCIEX Technologies, USA) was recommended to visualize raw data of target components in two-stage mass-to-charge ratio map. Then, based on fragment ion information, such components were identified by comparing to HMDB (http://www.hmdb.ca/), PubChem (https://pubchem.ncbi.nlm.nih.gov/), NIST (https://www.nist.gov/), MassBank (http://www.massbank.jp/) and METLIN (https://metlin.scripps.edu/) databases.
Ion Mode:NEGATIVE
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