|
| Status |
Public on Oct 16, 2024 |
| Title |
Gm.3hai.biorep1.run2 |
| Sample type |
SRA |
| |
|
| Source name |
whole seed
|
| Organism |
Glycine max |
| Characteristics |
tissue: whole seed
genotype: Williams 82
treatment: Gm seed at 3 hours after imbibition
|
| Growth protocol |
Long day condition (16 hours light, 8 hours dark) at 22 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were collected from early, mid and late desiccation, mature dry seeds, and 3hai (hour after imbibition), 16hai and 27hai. Total RNA was extracted using RNAeasy kit (Qiagen) plus in-column DNase digestion.
Illumina cDNA libraries were constructed with the Illumina Tru-Seq RNA Prep kit per manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina raw reads were first trimmed at 5' and 3' ends with the positions error rates > 0.5%, trimmed 10 bases average error rate > 0.1% and trimmed the adapter using trimmomatic (v0.38). The trimmed RNA reads were mapped to soybean reference genome (v1.1; https://phytozome-next.jgi.doe.gov) using Hisat2.ESeq2 was used to identify differentially expressed genes.
Assembly: soybean reference genome v1.1
Supplementary files format and content: tab-delimited text file of normalized count matrix
|
| |
|
| Submission date |
Nov 20, 2023 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Tzung-Fu Hsieh |
| E-mail(s) |
[email protected]
|
| Phone |
7042505467
|
| Organization name |
North Carolina State University
|
| Department |
Plant and Microbial Biology
|
| Street address |
Tzung-Fu Hsieh, 600 Laureate Way
|
| City |
Kannapolis |
| State/province |
NC |
| ZIP/Postal code |
28081 |
| Country |
USA |
| |
|
| Platform ID |
GPL28801 |
| Series (1) |
| GSE248224 |
Dissecting the temporal genetic networks programming soybean embryo development from embryonic morphogenesis to post-germination |
|
| Relations |
| BioSample |
SAMN38329608 |
| SRA |
SRX22581674 |
