|
| Status |
Public on Sep 18, 2022 |
| Title |
Combined water deficit and heat stress pod replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Pods
|
| Organism |
Glycine max |
| Characteristics |
tissue: Pods
cultivar: Magellan
treatment: Water deficit and heat stress
|
| Treatment protocol |
At R1, plants were randomly divided into control (CT), and 3 stress categories as water-deficit (WD), heat stress (HS), and combination of water-deficit and heat stress (WD+HS) in four different BDR16 growth chambers placed side-by-side in the same room. The relative humidity of chambers was maintained at about 50-60% in all chambers. The plants under WD and WD+HS treatments were irrigated with only 30% of the water available for, while plants in the CT and HS treatments were irrigated with 100% of the water available for transpiration. For HS and WD+HS treatments, temperature of chambers was maintained to 38 °C Day and 28 °C night temperature by ramping the temperature between 6.00-8.00 AM and decreasing it down to 28 °C between 16.00-20.00 PM.
|
| Growth protocol |
Soybean (Glycine max, cv Magellan) seeds were inoculated with Bradyrhizobium japonicum inoculum and germinated in Promix BX for a week in a growth chamber under short day growth condition (12-h light/12-h dark), at 28/24 ℃ day/night temperature and 500 μmol photons m-2 s-1. The temperature of the chambers was ramped from 24 to 28 °C between 6.00-8.00 AM and decreased to 24 °C from 16.00-20.00 PM. Seedlings were transplanted into pots containing 1 kg mixture of Promix BX and perlite mixed in ratio of 10:1 and soaked in 1 l of water-fertilizer mix (Zack’s classic blossom booster 10-30-20) . Plants were then grown under 28/24 ℃ day/night temperatures and 1000 μmol photons m-2 s-1 light intensity (12-h light/12-h dark photoperiod) for the next 16-18 days (until start of first open flower, R1 developmental stage) while irrigating twice a week with Zack’s classic blossom booster 10-30-20 fertilizer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Soybean pods were collected from plants and immediately frozen in liquid nitrogen. About 10-15 pods were pooled together from 8-10 different plants for each biological repeat and total RNA was isolated using Qiagen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HDPO3
|
| Data processing |
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to G_max V2.1 whole genome using Hisat2 V2.2.1.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 20110.
Assembly: Glycine_max_v2.1.51
Supplementary files format and content: replicatewise_fpkm.txt: Matrix table of FPKM values for all samples.
Supplementary files format and content: replicatewise_readcounts.txt: Matrix table of Raw counts values for all samples.
|
| |
|
| Submission date |
Sep 15, 2022 |
| Last update date |
Sep 18, 2022 |
| Contact name |
Ron Mittler |
| E-mail(s) |
[email protected]
|
| Organization name |
The Division of Plant Sciences and Technology
|
| Department |
Christopher S. Bond Life Sciences Center
|
| Lab |
LSC 312
|
| Street address |
University of Missouri,1201 Rollins St
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65201 |
| Country |
USA |
| |
|
| Platform ID |
GPL28801 |
| Series (1) |
| GSE213479 |
Differential transpiration of pods during stress combination in soybean |
|
| Relations |
| BioSample |
SAMN30876642 |
| SRA |
SRX17596853 |
