|
| Status |
Public on Jul 22, 2019 |
| Title |
Z-1: WT rep1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Glycine max |
| Characteristics |
tissue: Soybean root cells
|
| Treatment protocol |
For the salt stress treatment, the uniformly growing plants were kept in 0 mM/L, 50 mM/L, 75 mM/L, 100 mM/L, 150 mM/L and 200 mM/L of NaCl solutions for 30 hours.
|
| Growth protocol |
The Glycine line, Glycine max Williams 82, was used in this study. Seeds were sterilized with 75% ethanol and then germinated in pots filled with coconut fiber. Soybean seedlings were grown in soil in an incubator with 25℃/20℃ (light/dark) and 16h/8h (light/dark) cycles until the second trifoliate leaves started expand. As a control, the untreated seedlings (0 mM/L) were planted and harvested at the same time with the stress-treated plants. The 100 mM/L salt treated seedlings were used for RNA-seq and ChIP-seq analysis since the phenotypic differences were clear at this concentration which is also commonly used for salinity test on soybean.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the root of soybeans with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
Library making, RNA-seq and data analysis were performed as described previously (Xu et al., 2018).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Paired-end reads were generated with the Illumina HiSeq 2500 system.
The RNA sequencing reads were aligned to the Glycine max reference genome (Glycine max Wm82.a2.v1) using TopHat2 (Kim et al., 2013). Genes that met the criterion of a detectable expression signal in control or salt plants were further analyzed.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: The fold change (FC) was calculated by comparing the expression level of the salt samples to control (salt/control). Briefly, the ‘‘|Log2FC|>1 and p-adj < 0.05’’ was used as the threshold to judge the significance of gene expression difference. Genes that display a greater than 2-FC in the salt-treated were designated as up- or down-regulated if the salt RNA level was higher or lower than that of control plants, respectively.
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Jul 22, 2019 |
| Contact name |
guoweijun guoweijun |
| E-mail(s) |
guoweijun01@163.com
|
| Phone |
13126571191
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Department |
Biotechnology Research Institute
|
| Lab |
LI PU lab
|
| Street address |
No. 12, Zhongguancun South Street
|
| City |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL21309 |
| Series (2) |
| GSE133574 |
Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (RNA-seq dataset) |
| GSE133575 |
Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress |
|
| Relations |
| BioSample |
SAMN12172108 |
| SRA |
SRX6385188 |
