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| Status |
Public on Aug 01, 2022 |
| Title |
non-elongating 6 day rep 1 (JA43) |
| Sample type |
SRA |
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| Source name |
non-elongating 6 day
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| Organism |
Oryza sativa |
| Characteristics |
genotype: M202(Sub1)
tissue: non-elongating leaves
treatment: submergence
time: 6 day
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| Treatment protocol |
Plants were completely submerged for 0, 1, 3, and 6 days. Immediately after de-submergence at each time point, the 5th (elongating) leaves and lower (non-elongating) leaves were separated, frozen in liquid nitrogen, and stored at -80C until use.
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| Growth protocol |
Rice plants were grown in pots in a greenhouse until the 4.2-leaf stage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from frozen tissues using a miRNeasy Mini kit (Qiagen, Hilden, Germany). Genomic DNA was eliminated by on-column digestion.
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
paired-end
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
JA43
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| Data processing |
raw reads were mapped using STAR, number of mapped reads were counted using featureCounts and differentially expressed genes were identified using DESeq2
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: ReadCounts_022017.xlsx
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| Submission date |
Aug 02, 2021 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Song Li |
| E-mail(s) |
songli@vt.edu
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| Phone |
5402312756
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| Organization name |
Virginia Tech
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| Street address |
1220A, 1880 Pratt Dr.
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| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE181336 |
Transcriptomic responses to submergence in elongating and non-elongating leaves of rice with and without SUB1A |
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| Relations |
| BioSample |
SAMN20522462 |
| SRA |
SRX11632557 |
| 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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