Summary of Study ST003350
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 PR002084. The data can be accessed directly via it's Project DOI: 10.21228/M87K0X 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 | ST003350 |
Study Title | Dissecting the Genetic Basis of UV-B Responsive Metabolites in Rice |
Study Summary | UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the biochemical and genetic basis of the metabolome underlying the response to UV-B stress remain elusive in rice. In this study, we performed comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal-light conditions using a widely targeted metabolomics approach. Our results revealed substantial differences in the accumulation of metabolites between the two major rice subspecies indica and japonica, especially after UV-B treatment, shedding light on the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response. |
Institute | Industrial Crops Institute of Hubei Academy of Agricultural Sciences |
Last Name | Zhang |
First Name | Feng |
Address | 43 nanhu road, hongshan district, wuhan city, hubei province, Wuhan, Hubei,430064,China |
zhangfeng2023@hbaas.ac.cn | |
Phone | 027-15926268746 |
Submit Date | 2024-06-18 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2024-08-12 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR002084 |
Project DOI: | doi: 10.21228/M87K0X |
Project Title: | Metabolics studies under UV-B conditions in rice leaf |
Project Summary: | We performed comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal-light conditions using a widely targeted metabolomics approach |
Institute: | Industrial Crops Institute of Hubei Academy of Agricultural Sciences |
Last Name: | Zhang |
First Name: | Feng |
Address: | 43 Nanhu road, Hongshan district, wuhan city, Hubei province, Wuhan, Hubei, 430064, China |
Email: | zhangfeng2023@hbaas.ac.cn |
Phone: | 027-15926268746 |
Subject:
Subject ID: | SU003471 |
Subject Type: | Plant |
Subject Species: | Oryza sativa |
Taxonomy ID: | 4530 |
Species Group: | Plants |
Factors:
Subject type: Plant; Subject species: Oryza sativa (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample source | Theatment |
---|---|---|---|
SA365356 | ma249-305-p-1 | Rice | CK |
SA365357 | ma249-276-p-1 | Rice | CK |
SA365358 | ma249-279-p-1 | Rice | CK |
SA365359 | ma249-281-p-1 | Rice | CK |
SA365360 | ma249-283-p-1 | Rice | CK |
SA365361 | ma249-284-p-1 | Rice | CK |
SA365362 | ma249-287-p-1 | Rice | CK |
SA365363 | ma249-294-p-1 | Rice | CK |
SA365364 | ma249-307-p-1 | Rice | CK |
SA365365 | ma249-271-p-1 | Rice | CK |
SA365366 | ma249-308-p-1 | Rice | CK |
SA365367 | ma249-311-p-1 | Rice | CK |
SA365368 | ma249-312-p-1 | Rice | CK |
SA365369 | ma249-313-p-1 | Rice | CK |
SA365370 | ma249-314-p-1 | Rice | CK |
SA365371 | ma249-318-p-1 | Rice | CK |
SA365372 | ma249-321-p-1 | Rice | CK |
SA365373 | ma249-275-p-1 | Rice | CK |
SA365374 | ma249-269-p-1 | Rice | CK |
SA365375 | ma249-324-p-1 | Rice | CK |
SA365376 | ma249-237-p-1 | Rice | CK |
SA365377 | ma249-213-p-1 | Rice | CK |
SA365378 | ma249-222-p-1 | Rice | CK |
SA365379 | ma249-224-p-1 | Rice | CK |
SA365380 | ma249-227-p-1 | Rice | CK |
SA365381 | ma249-230-p-1 | Rice | CK |
SA365382 | ma249-231-p-1 | Rice | CK |
SA365383 | ma249-233-p-1 | Rice | CK |
SA365384 | ma249-239-p-1 | Rice | CK |
SA365385 | ma249-267-p-1 | Rice | CK |
SA365386 | ma249-243-p-1 | Rice | CK |
SA365387 | ma249-244-p-1 | Rice | CK |
SA365388 | ma249-250-p-1 | Rice | CK |
SA365389 | ma249-255-p-1 | Rice | CK |
SA365390 | ma249-258-p-1 | Rice | CK |
SA365391 | ma249-259-p-1 | Rice | CK |
SA365392 | ma249-266-p-1 | Rice | CK |
SA365393 | ma249-322-p-1 | Rice | CK |
SA365394 | ma249-325-p-1 | Rice | CK |
SA365395 | ma249-206-p-1 | Rice | CK |
SA365396 | ma249-489-p-1 | Rice | CK |
SA365397 | ma249-463-p-1 | Rice | CK |
SA365398 | ma249-466-p-1 | Rice | CK |
SA365399 | ma249-468-p-1 | Rice | CK |
SA365400 | ma249-469-p-1 | Rice | CK |
SA365401 | ma249-471-p-1 | Rice | CK |
SA365402 | ma249-481-p-1 | Rice | CK |
SA365403 | ma249-484-p-1 | Rice | CK |
SA365404 | ma249-490-p-1 | Rice | CK |
SA365405 | ma249-459-p-1 | Rice | CK |
SA365406 | ma249-494-p-1 | Rice | CK |
SA365407 | ma249-498-p-1 | Rice | CK |
SA365408 | ma249-499-p-1 | Rice | CK |
SA365409 | ma249-503-p-1 | Rice | CK |
SA365410 | ma249-506-p-1 | Rice | CK |
SA365411 | ma249-517-p-1 | Rice | CK |
SA365412 | ma249-006-p-1 | Rice | CK |
SA365413 | ma249-461-p-1 | Rice | CK |
SA365414 | ma249-455-p-1 | Rice | CK |
SA365415 | ma249-332-p-1 | Rice | CK |
SA365416 | ma249-376-p-1 | Rice | CK |
SA365417 | ma249-338-p-1 | Rice | CK |
SA365418 | ma249-345-p-1 | Rice | CK |
SA365419 | ma249-347-p-1 | Rice | CK |
SA365420 | ma249-348-p-1 | Rice | CK |
SA365421 | ma249-349-p-1 | Rice | CK |
SA365422 | ma249-356-p-1 | Rice | CK |
SA365423 | ma249-361-p-1 | Rice | CK |
SA365424 | ma249-383-p-1 | Rice | CK |
SA365425 | ma249-452-p-1 | Rice | CK |
SA365426 | ma249-396-p-1 | Rice | CK |
SA365427 | ma249-397-p-1 | Rice | CK |
SA365428 | ma249-419-p-1 | Rice | CK |
SA365429 | ma249-422-p-1 | Rice | CK |
SA365430 | ma249-425-p-1 | Rice | CK |
SA365431 | ma249-429-p-1 | Rice | CK |
SA365432 | ma249-441-p-1 | Rice | CK |
SA365433 | ma249-442-p-1 | Rice | CK |
SA365434 | ma249-211-p-1 | Rice | CK |
SA365435 | ma249-001-p-1 | Rice | CK |
SA365436 | ma249-205-p-1 | Rice | CK |
SA365437 | ma249-073-p-1 | Rice | CK |
SA365438 | ma249-057-p-1 | Rice | CK |
SA365439 | ma249-062-p-1 | Rice | CK |
SA365440 | ma249-063-p-1 | Rice | CK |
SA365441 | ma249-066-p-1 | Rice | CK |
SA365442 | ma249-067-p-1 | Rice | CK |
SA365443 | ma249-068-p-1 | Rice | CK |
SA365444 | ma249-072-p-1 | Rice | CK |
SA365445 | ma249-074-p-1 | Rice | CK |
SA365446 | ma249-048-p-1 | Rice | CK |
SA365447 | ma249-075-p-1 | Rice | CK |
SA365448 | ma249-076-p-1 | Rice | CK |
SA365449 | ma249-078-p-1 | Rice | CK |
SA365450 | ma249-079-p-1 | Rice | CK |
SA365451 | ma249-080-p-1 | Rice | CK |
SA365452 | ma249-082-p-1 | Rice | CK |
SA365453 | ma249-083-p-1 | Rice | CK |
SA365454 | ma249-054-p-1 | Rice | CK |
SA365455 | ma249-047-p-1 | Rice | CK |
Collection:
Collection ID: | CO003464 |
Collection Summary: | The fully expanded leaves of at least three lines from each variety in UV-B and normal conditions were harvested and snap-frozen in liquid nitrogen and stored at −80 °C for a metabolite sample and every sample was repeated two times. |
Sample Type: | Leaves |
Treatment:
Treatment ID: | TR003480 |
Treatment Summary: | 160 rice accessions were selected for UV-B stress, which included 76 Indica, 58 Japonica, 3 Admix, 17 Aus and 6 VI based on the proportion of rice different subgroups in the 533 rice varieties from all over the world. Information about these accessions, including variety name and place of origin are listed in Supplementary_Table3.xlsx. The 160 rice accessions were sown and grown in a growth pool in Huazhong Agricultural University, Wuhan. After one week, each variety was divided into two groups respectively and grown in two areas with equal condition. Four weeks later, rice seedlings in one area were moved to a UV-B chamber (TL40W/302 nm narrowband UV-B tube, Philips, Netherlands) with 30 μW cm−2 UV-B intensity. UV-B intensity was detected by a UV radiometer with the UV-295 detector from the photoelectric instrument factory (Beijing Normal University, China). The CK samples were not treated with UV-B. |
Sample Preparation:
Sampleprep ID: | SP003478 |
Sampleprep Summary: | 100 mg powder was weighed and extracted overnight at 4°C with 1.0 ml of 70% aqueous methanol (methanol: H2O, 70:30, v/v) |
Combined analysis:
Analysis ID | AN005491 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | SHIMADZU LC-20A |
Column | Shimadzu Shim-pack VP-ODS C18 (150 x 2mm, 5um) |
MS Type | ESI |
MS instrument type | QTRAP |
MS instrument name | Applied Biosystems 4000 Q TRAP |
Ion Mode | POSITIVE |
Units | Relative intensity |
Chromatography:
Chromatography ID: | CH004174 |
Chromatography Summary: | HPLC, Shim-pack UFLC SHIMADZU CBM20A system; shim-pack VP-ODS C18 (particle size 5.0μm, length 2×150mm) |
Instrument Name: | SHIMADZU LC-20A |
Column Name: | Shimadzu Shim-pack VP-ODS C18 (150 x 2mm, 5um) |
Column Temperature: | 40 |
Flow Gradient: | 100:0 (A:B) V/V at 0 min, 5:95 (A:B) V/V at 20.0 min, 5:95 (A:B) V/V at 22.0 min, 95:5 (A:B) V/V at 22.1 min, 95:5 (A:B) V/V at 25.0 min |
Flow Rate: | 0.25mL/min |
Solvent A: | 100% water; 0.04% acetic acid |
Solvent B: | 100% acetonitrile; 0.04% acetic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS005217 |
Analysis ID: | AN005491 |
Instrument Name: | Applied Biosystems 4000 Q TRAP |
Instrument Type: | QTRAP |
MS Type: | ESI |
MS Comments: | - |
Ion Mode: | POSITIVE |
Analysis Protocol File: | ZF_MS_method.pdf |