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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 14, 2023 |
| Title |
L8, DR, Day2, rpt3 |
| Sample type |
SRA |
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| Source name |
Spikelet
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: Spikelet
line: L8
genotype: TaPYLox
treatment: Drought
time: Day2
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| Treatment protocol |
The water supply was stopped for drought-treated samples (DR2, 5, 7, and 9) and continued for the well-watered ones (WTR2, 5, 7, and 9).
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| Growth protocol |
The plants were cultivated at 25°C (14-h light)/15°C (10-h dark), with relative humidity levels of 40% (light)/60% (dark) until anthesis.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol from frozen spikelets. 6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEXTflex Rapid DIR mRNA Bundle following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The raw sequence data were trimmed and qualified by trimmomatic (version 0.39) with default parameters.
The clean reads were aligned to the primary transcripts of the wheat reference genome by kallisto (version 0.46.2) with default parameters.
Assembly: IWGSC (ensembl49)
Supplementary files format and content: A fileset (an HDF5 and a tab-delimited table files for transcript abundance, and a JSON file for running log) for each kallisto run.
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| Submission date |
Mar 14, 2023 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Ryosuke Mega |
| E-mail(s) |
mega@yamaguchi-u.ac.jp
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| Organization name |
Yamaguchi University
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| Street address |
1677-1, Yoshida
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| City |
Yamaguchi |
| ZIP/Postal code |
753-8515 |
| Country |
Japan |
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| Platform ID |
GPL25409 |
| Series (1) |
| GSE227374 |
Transcriptomic profile of wheat seed development under progressive drought conditions |
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| Relations |
| BioSample |
SAMN33761536 |
| SRA |
SRX19678872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7099152_L8D1-3.tar.gz |
17.3 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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