|
| Status |
Public on Oct 30, 2024 |
| Title |
WT_10DAG_NaCl_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis |
| Characteristics |
tissue: whole seedlings
genotype: WT (Col-0)
treatment: 150 mM NaCl for 1, 2, and 4 h
|
| Treatment protocol |
10-day-old WT seedlings grown under SD conditions (8-h-light/16-h-dark cycle) were placed on filter papers soaked in MS solution containing 150 mM NaCl. After 0, 1, 2, and 4 h, the seedlings were harvested and prepared as whole seedlings.
|
| Growth protocol |
Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 2 d at 4℃. The seeds were sown on 0.7% (w/v) agar plates containing on-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22℃ under SD conditions (8-h-light/16-h-dark cycle).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using with RNAqueous Kit with Plant RNA Isolation Aid (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 150 mM NaCl treatment. Whole seedlings were sampled and total RNA was analyzed.
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10.1 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 28, 2024 |
| Last update date |
Oct 30, 2024 |
| Contact name |
Yong-Hwan Moon |
| E-mail(s) |
[email protected]
|
| Phone |
+82515102592
|
| Organization name |
Pusan National University
|
| Department |
Molecular Biology
|
| Lab |
Plant Molecular Genetics Lab
|
| Street address |
Busandaehak-ro 63Beon-gil 2, Geumjeong-gu
|
| City |
Busan |
| ZIP/Postal code |
46241 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL27784 |
| Series (1) |
| GSE275862 |
Differentially expressed genes between WT and AtC3H3 OX, and WT and AtC3H26 OX |
|
| Relations |
| BioSample |
SAMN43392614 |
| SRA |
SRX25853385 |
