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Status |
Public on Aug 01, 2022 |
Title |
non-elongating 3 day rep 1 (JA25) |
Sample type |
SRA |
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Source name |
non-elongating 3 day
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Organism |
Oryza sativa |
Characteristics |
genotype: M202 tissue: non-elongating leaves treatment: submergence time: 3 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 |
JA25
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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 |
SAMN20522491 |
SRA |
SRX11632536 |
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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