|
| Status |
Public on May 28, 2021 |
| Title |
PPZ rep2 |
| Sample type |
SRA |
| |
|
| Source name |
0.1 μM PPZ_treatment_Root
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Wm82
age: ten and a half days seedlings
treatment: 0.1 μM PPZ treatment
tissue: 1 cm of the root tip
|
| Treatment protocol |
3-day-old soybean seedlings were transferred to hydroponics medium for 5 days, then treated with 0.1 μM PPZ and mock for another 2.5 days. Meanwhile, 3-day-old soybean seedlings were transferred to hydroponics medium for 7 days, then treated with 0.01 nM BL and mock for another 0.5 days.
|
| Growth protocol |
Soybean seeds for RNA-seq were germinated in vermiculite for 3 days. Then seedlings were transferred into modified half-strength Hoagland's nutrient solution under long-day conditions (16 h light / 8 h dark) at 24 °C for 7 and a half days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated of soybean seedlings root tips(1 cm) by using RNAprep pure Plant Kit (TIANGEN, China).
RNA degradation and contamination was detection on 1% agarose gels. The purity of RNA was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. RNA libraries were constructed by 1 μg total RNA per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PPZ2
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Raw data filtering steps contain removing reads containing adapter, reads containing ploy-N and low quality reads to obtain clean reads. Meanwhile, Q20, Q30 and GC content the clean data were calculated.
Paired-end clean reads were aligned to Glycine max whole genome using Hisat2 v2.0.5 software.
FeatureCounts v1.5.0-p3 was used to calculate the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was used by DESeq2 software.
Genome_build: Glycine_max_Wm82.a4.v1.gtf
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 26, 2021 |
| Last update date |
May 28, 2021 |
| Contact name |
wenfei Wang |
| E-mail(s) |
[email protected]
|
| Phone |
13685023625
|
| Organization name |
Fujian Agriculture and Forestry University
|
| Department |
Haixia Institute of Science and Technology
|
| Street address |
No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China
|
| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350002 |
| Country |
China |
| |
|
| Platform ID |
GPL28801 |
| Series (1) |
| GSE175586 |
Transcriptomic profiling of brassinosteroids response genes in soybean (Glycine max L.) |
|
| Relations |
| BioSample |
SAMN19355595 |
| SRA |
SRX11001719 |
