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| Status |
Public on May 23, 2020 |
| Title |
NIL_APO1_YP_3 |
| Sample type |
SRA |
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| Source name |
Oryza sativa
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| Organism |
Oryza sativa |
| Characteristics |
tissue: Young panicles
genotype: Pbl6 [APO1]
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from young panicle as described by Sambrook et al. (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning: a laboratory manual. Mol. cloning a Lab. manual. (1989).)
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 NextSeq 500 |
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| Data processing |
convert .bcl files to .fastq using bcl2fastq
mask bases with QV < 25 using original script
align reads to cDNA reference provided from IRGSP1using bowtie with options "--all --best --strata"
count reads using linux commands (sort and uniq)
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.csv
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| Submission date |
May 22, 2020 |
| Last update date |
May 23, 2020 |
| Contact name |
Tokunori Hobo |
| Organization name |
Nagoya University
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| Street address |
Furo-cho, Chikusa-ku
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| City |
Nagoya |
| ZIP/Postal code |
464-8601 |
| Country |
Japan |
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| Platform ID |
GPL21087 |
| Series (1) |
| GSE151043 |
Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles |
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| Relations |
| BioSample |
SAMN14997772 |
| SRA |
SRX8380640 |
| 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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