|
| Status |
Public on Mar 13, 2024 |
| Title |
W3H150m_rep2_MGF |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: fruit
treatment: water_3day_heat_150m
|
| Treatment protocol |
Sixteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 3 days. After ethanol pretreatment, the pots were placed in an air incubator set at 50 °C and maintained for the indicated time periods as heat stress treatment. During the heat stress treatment, the pots were electrically rotated in the air incubator to avoid the local effect. After the heat stress treatment, the pots were returned to the growth room and maintained for the indicated time periods.
|
| Growth protocol |
Seeds of a tomato (Solanum lycopersicum L.) cultivar, “Micro-Tom” were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using purelink Plant RNA Reagent (Thermo Fisher Scientifc Inc., Waltham, MA, USA).
The sequencing library was prepared using the Lasy-Seq method (Kamitani et al. 2019). Specifically, 200 ng of total RNA was used per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: ITAG4.0
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample
Supplementary files format and content: Tab-delimited text files include normalized count values for each sample
|
| |
|
| Submission date |
Oct 16, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
motoaki seki |
| Organization name |
RIKEN
|
| Department |
CSRS
|
| Lab |
Plant Genomic Network Research Team
|
| Street address |
Suehiro-cho 1-7-22, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24124 |
| Series (1) |
| GSE245512 |
Determination of transcriptomic changes associated with heat stress in ethanol treated vs non-treated control tomato plants II |
|
| Relations |
| BioSample |
SAMN37849476 |
| SRA |
SRX22106489 |
