|
| Status |
Public on Nov 01, 2014 |
| Title |
Na6hrR2 |
| Sample type |
SRA |
| |
|
| Source name |
roots
|
| Organism |
Glycine max |
| Characteristics |
genotype: Williams 82
developmental stage: V1 stage seedlings
tissue: root
|
| Treatment protocol |
The salt treatment was applied by transferring the seedlings into 100 mM NaCl solution. For the dehydration treatment, plants were removed from the germination paper and left in air under water-limiting conditions to impose dehydration stress.
|
| Growth protocol |
The seeds of G. max cv. Williams 82 were germinated on moist germination paper and were allowed to grow until the v1 stage (first trifoliolate stage) in a growth chamber maintained at 77 F and 60% humidity throughout the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Root tissue was harvested, flash frozen in liquid nitrogen, and total RNA was isolated using Qiagen RNeasy® Plant mini kit per the manufacturer’s protocol. The RNA samples were treated with Ambion® TURBO DNA-free™ DNase to get rid of any DNA contamination in the RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Salt stress 6 hr replicate 2
|
| Data processing |
The reads were aligned with GSNAP (Wu TD and Nacu S, Bioinformatics, 2010) using default settings with a maximum of 4 mis-matches allowed.
The uniquely mapped reads that mapped to a single location in the genome were analyzed for differential gene expression between the control and treatment samples using the R package DESeq v1.7.10 (Anders S and Huber W, Genome Biology, 2010).
Genome_build: Glycine max genome assembly and annotation v1.01 from Phytozome (JGI Glyma1.0 gene calls).
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each gene
Supplementary_files_format_and_content: tab-delimited text file includes DESeq normalized counts for each gene
|
| |
|
| Submission date |
May 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven B Cannon |
| E-mail(s) |
steven.cannon@ars.usda.gov
|
| Organization name |
United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit
|
| Street address |
Crop Genome Informatics Laboratory #1017, Iowa State University
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL15008 |
| Series (1) |
| GSE57252 |
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress |
|
| Relations |
| BioSample |
SAMN02742647 |
| SRA |
SRX531085 |
