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| Status |
Public on Sep 01, 2023 |
| Title |
Control_0h3 |
| Sample type |
SRA |
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| Source name |
aerial tissue
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| Organism |
Lactuca sativa |
| Characteristics |
cultivar: Salinas
age: 18 days
tissue: aerial tissue
treatment: warm-grown
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| Treatment protocol |
Abiotic stress treatments were conducted on eighteen-day-old plants. For cold treatment, plants were exposed to low temperature (4°C) for 4 h, 24 h, or 7 days. For high salt stress conditions, plants were treated with 250 mM NaCl. For heat stress conditions, plants were exposed to 34 °C. For drought stress conditions, watering was withheld after ensuring all excess water was drained and absorbed by paper towels from the pots. Following exposure to these stress conditions, leaf samples were collected at 0 h, 5 h, 24 h, and 48 h for each treatment, with the 0 h samples serving as controls.
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| Growth protocol |
Plants were grown on soil in pots in a growth chamber at 20°C under a 16-h photoperiod with a light intensity of 350-400 μmol m−2 sec−1.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated for each experimental replicate using Plant RNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Ls_abiotic_cpm_value.csv
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and those with N (based underterminded) > 10% or low quality bases (Qscore <=5) >50% were removed.
The filtered reads were mapped to lettuce (v8) whole genome using STAR v2.5.2 with default parameters; the resulting BAM files were used to count reads at the gene-level using featureCounts.
Counts per million (CPM) mapped reads for each of biological samples were calculated using edgeR based on raw counts of STAR.
Assembly: version8; id 37106
Supplementary files format and content: A comma-delimited text files includes CPM values for each of samples
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| Submission date |
Aug 23, 2023 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Sunchung Park |
| E-mail(s) |
Sunchung.park@usda.gov
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| Organization name |
USDA -ARS
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| Department |
ARS-NEA
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| Lab |
SPCL
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| Street address |
10300 Baltimore ave, Bldg001
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| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
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| Platform ID |
GPL26895 |
| Series (1) |
| GSE241604 |
Transcriptome profiling of lettuce plants exposed to abiotic stresses |
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| Relations |
| BioSample |
SAMN37131238 |
| SRA |
SRX21475099 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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