|
| Status |
Public on Jan 01, 2024 |
| Title |
ZH11_1 |
| Sample type |
SRA |
| |
|
| Source name |
whole-plant
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: whole-plant
genotype: wild-type
treatment: untreated
|
| Treatment protocol |
Treatment started with the addition of 2-nitroaniline (0.8 mM) and seedlings were kept under standard physiological conditions at 25°C. After 8 h of treatment, samples were collected and stored at -80 °C.
|
| Growth protocol |
The rice seedlings were grown in the hydroponic medium for two weeks before 2-nitroaniline treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent (Invitrogen, USA). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Data were processed using the online platform of Majorbio Cloud Platform (www.majorbio.com)
SeqPrep was used to strip adaptors and/or merging paired reads with overlap into single reads (https://github.com/jstjohn/SeqPrep)
Sickle was used to remove low-quality reads (https://github.com/najoshi/sickle).
Cufflinks (Version 2.2.1) was used to assemble the clean data which were then mapped to the rice reference genome
Gene expression levels were determined with the Transcripts Per Million reads (TPM) method
Assembly: Rice Genome Annotation Project (http://rice.uga.edu/)
Supplementary files format and content: xlsx files include gene annotations and TPM values for each Sample
|
| |
|
| Submission date |
Apr 24, 2022 |
| Last update date |
Jan 26, 2024 |
| Contact name |
zhenjun li |
| E-mail(s) |
zhenjun_1234@aliyun.com
|
| Organization name |
Shanghai academy of agricultural sciences
|
| Street address |
Beidi rd 2901
|
| City |
Shanghai |
| ZIP/Postal code |
201106 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE201399 |
Transcriptome profiling of rice plants in response to 2-Nitroaniline |
|
| Relations |
| BioSample |
SAMN27754302 |
| SRA |
SRX14985447 |
