|
| Status |
Public on Jul 08, 2021 |
| Title |
ma3 |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Zea mays |
| Characteristics |
develpmental stage and tissue: V3 seedling shoots
treatment: Treated with ABA 50 microM for 1 h
genotype: mop1-1 homozygous mutant
|
| Treatment protocol |
Maize seedlings at the V3 stage were removed from the soil, roots were rinsed in water, dried and then submerged in a 1 L beaker with 250 mL of liquid Murashige and Skoog (MS) media (Sigma Aldrich, M6899) with 50 μM ABA (ABA; (Sigma Aldrich, (+/-) Abscisic Acid, A1049)) or without ABA (MS) for 1 hour.
|
| Growth protocol |
Maize plants were grown in greenhouse conditions (16 h light period, 25°C, 50% humidity) until V3 stage was reached.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Seedling shoots were flash frozen and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit from Illumina (NEB #E7770) was used with 1 µg of RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Paired-end 150 bp (PE 150) RNA-sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
none
|
| Data processing |
Illumina base-calling
FASTQ adapters were trimmed and read quality control was assessed using fastp (0.21.0). Reads were mapped to the B73 maize genome (AGP B73v4) (Jiao et al. 2017) by HISAT2 v2.2.1 (Pertea et al. 2016).
Transcripts were assembled de novo to allow for inclusion of transcripts that are not included in the reference genome annotation and quantified using StringTie v2.1.4 (Pertea et al. 2016). Gene count matrices were generated from this data using the prepDE.py python script available in the StringTie website.
Genome_build: AGPv.4 B73
Supplementary_files_format_and_content: comma separated values files include gene counts for each Sample
|
| |
|
| Submission date |
Jul 07, 2021 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Thelma F Madzima |
| E-mail(s) |
madzima@uw.edu
|
| Phone |
425-352-5176
|
| Organization name |
University of Washington Bothell
|
| Department |
Division of Biological Sciences
|
| Street address |
18115 Campus Way NE
|
| City |
Bothell |
| State/province |
WA |
| ZIP/Postal code |
98011-8246 |
| Country |
USA |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE179629 |
Direct and indirect transcriptional effects of abiotic stress in Zea mays plants defective in RNA-directed DNA methylation |
|
| Relations |
| BioSample |
SAMN20090102 |
| SRA |
SRX11368848 |
