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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST001194 |
| Study Title | Flavonoid study of Ginkgo leaves facing to different elevation and plant age |
| Study Summary | Ginkgo 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 Name | Zou |
| First Name | Kai |
| Address | Central South University, 932 Lushan South Road, Yuelu District, Changsha City, Hunan Province |
| zoukai3412085@hotmail.com | |
| Phone | +8615273119784 |
| Submit Date | 2019-05-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-07-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|---|
| SA083085 | HO-2 | High | Old |
| SA083086 | HO-1 | High | Old |
| SA083087 | HO-3 | High | Old |
| SA083088 | HY-3 | High | Young |
| SA083089 | HY-1 | High | Young |
| SA083090 | HY-2 | High | Young |
| SA083091 | LO-3 | Low | Old |
| SA083092 | LO-1 | Low | Old |
| SA083093 | LO-2 | Low | Old |
| SA083094 | LY-2 | Low | Young |
| SA083095 | LY-1 | Low | Young |
| SA083096 | LY-3 | Low | 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 quadrupole |
| 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 quadrupole |
| 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 |
