|
| Status |
Public on Mar 22, 2020 |
| Title |
mut_m1_ms_3 |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Zea mays |
| Characteristics |
develpmental stage: V3
tissue: seedling shoots
treatment: MS
time point: 8 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 8 hours .
|
| 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 |
HiSeq X Ten |
| |
|
| Data processing |
Illumina base-calling
FASTQ adapters were trimmed by Cutadapt 1.8.1 and Quality Control was performed using FASTQC v0.11.2 . Reads were mapped to the B73 maize genome (AGP B73v4 version 40) by HISAT2 v2.04
Transcripts were assembled and quantified using Stringtie v1.3.4d. Gene count matrices were generated from this data using the prepDE.py python script available in the Stringtie website
Genome_build: AGPv B73
Supplementary_files_format_and_content: comma separated values files include gene counts for each Sample
|
| |
|
| Submission date |
Jun 04, 2019 |
| Last update date |
Mar 22, 2020 |
| 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 |
GPL25842 |
| Series (1) |
| GSE132167 |
Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1 |
|
| Relations |
| BioSample |
SAMN11957385 |
| SRA |
SRX5972311 |
