|
| Status |
Public on May 05, 2023 |
| Title |
soybean-root_t0-control_biol-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
2 cm root sections with roottip
|
| Organism |
Glycine max |
| Characteristics |
tissue: 2 cm root sections with roottip
treatment: no sucrose added
|
| Treatment protocol |
For sucrose treatment, 8.5 ml of 1 M sucrose (prepared in half-strength Hoagland solution) was added directly to the hydroponic solution, for a final concentration of 10 mM sucrose.
|
| Growth protocol |
Once the radicle reached 3 to 5 cm in length, germinatedsoybean seeds were transferred to containers containing about 850 ml half-strength Hoagland nutrient solution and were grown for 4 weeks;Hoagland solution was changed every 4 days. The growth chamber conditions were maintained at ~27℃ with a light cycle of 16 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plant Mini kit (Qiagen) was used for RNA extraction, following the protocol for “Purification of Total RNA from Plant Cells andTissues, and Filamentous Fungi“.
Using the Stranded mRNA Kit (Illumina), we converted the extracted RNA to cDNA, following the manufacturer’s instructions. Unique dual barcoding for each cDNA library was done using the IDT for Illumina RNA UD Indexes Set A (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CUSGm01_C
150 bp PE
|
| Data processing |
Illumina bcl2fastq2(v2.20) Conversion Software was used to demultiplex the obtained sequencing data and to convert base call files into FASTQ files.
Quality of sequences were checked by FastQC; adaptors and any low-quality sequences were removed with TRIMMOMATIC Version0.32
All paired RNA-seq reads were mapped to the reference genome of G. max cultivar Williams 82 using HISAT2, followed by StringTie
We used the prepDE.py3 script (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py3) to extract two csv (comma separated value) files with transcript and gene count information.
The normalized expression data FPKM (Fragment per kilobase and million) was extracted using the R package Ballgown
Assembly: Glycine max (assembly Glycine_max_v4.0)
Supplementary files format and content: normalized expression data FPKM (Fragment per kilobase and million) from all 9 cDNA libraries (t0, t20, t40, in 3 biologiical repliucations), extracted using the R package Ballgown
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
May 05, 2023 |
| Contact name |
Claudia Uhde-Stone |
| E-mail(s) |
[email protected]
|
| Organization name |
California State University, East Bay
|
| Department |
Biological Sciences
|
| Lab |
Stone lab
|
| Street address |
25800 Carlos Bee Blvd
|
| City |
Hayward |
| State/province |
CA |
| ZIP/Postal code |
94542 |
| Country |
USA |
| |
|
| Platform ID |
GPL28801 |
| Series (1) |
| GSE228888 |
Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses |
|
| Relations |
| BioSample |
SAMN34062145 |
| SRA |
SRX19859534 |
