biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsEui-Jung KimIllumina NovaSeq 6000RNA-seq of coding RNAOryza sativa Japonica GroupOryza sativa Japonica Grouphttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13984We created a triple loss-of-function/knockout mutant targeting three rice (Oryza sativa japonica) genes simultaneously via the Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR)/Cas9 system. The three selected genes are as follows: OsPRK1 (LOC_Os08g40990), OsPRK2 (LOC_Os06g45240), and OsPRK3 ((LOC_Os02g07810). These three OsPRKs are strongly transcriptional expressed in the mature anthers of rice (stages 13) and bi-/tricelluler pollen. The triple mutant of these OsPRKs does not produce self-fertilized seeds due to defects in the hydration and germination of pollen grains (male-sterile). This data is about RNA-sequencing transcriptome data about the Oryza sativa Dongjin used as a control and triple mutant of OsPRKs (OsPRK1/2/3). We sampled mature anther for the analysis.biostudies-arrayexpressSample Collection - Anthers that include bicellular and tricellular stages of pollen were collected (11 to 13 stages of Anthers).Library Construction - The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, \\"tagmentation\\" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.Sequencing - We used the Illumina platform to generate sequence reads and sequencing was done in such a way that each of the control and OsRALF17/19 groups includes three biological replicates. On average, six gb Illumina paired-end reads were produced for each sample. In the pipeline, the adapter trimming and read pre-processing was carried out using the trim_galore tool (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). After quality assessment of filtered reads with fastqc, reads were mapped to the Rice reference genome (RGAP version 7) using the Hisat2 aligner. The resultant read-mapped file was processed using featureCounts and DEGs were estimated from the raw count table using the DESeq2 package.Growth Protocol - Seeds of japonica rice (cv. Dongjin) of control and mutants were sterilized with 50% sodium hypochlorite and germinated in MS zero media in an incubator (14-h light/10-h dark, 28 °C (day)/22 °C (night), humidity 80%). After 1 week of germination, seedlings were transferred and grown in the greenhouse for 4 weeks under growth chamber conditions and transferred to the field.Nucleic Acid Extraction - Mature anthers were frozen directly in Liquid nitrogen and finely ground using mortar. Grounded samples were homogenized using TRI reagents (RNAiso, Takara) and BCP (1-bromo-3-chloropropane). DNA, RNA, and protein layers were separated by centrifugation. Then, total RNA was extracted using the RNeasy Mini Kit (QIAGEN).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesYu-Jin KimEui-Jung KimYe-jin SonKi-Hong JungfalseRNA sequencing of control and OsPRK1/2/3 triple knockout mutant in mature rice anthers (Oryza sativa japonica)We created a triple loss-of-function/knockout mutant targeting three rice (Oryza sativa japonica) genes simultaneously via the Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR)/Cas9 system. The three selected genes are as follows: OsPRK1 (LOC_Os08g40990), OsPRK2 (LOC_Os06g45240), and OsPRK3 ((LOC_Os02g07810). These three OsPRKs are strongly transcriptional expressed in the mature anthers of rice (stages 13) and bi-/tricelluler pollen. The triple mutant of these OsPRKs does not produce self-fertilized seeds due to defects in the hydration and germination of pollen grains (male-sterile). This data is about RNA-sequencing transcriptome data about the Oryza sativa Dongjin used as a control and triple mutant of OsPRKs (OsPRK1/2/3). We sampled mature anther for the analysis.2025-07-14T00:00:00Z2025-07-02T12:01:08.797Z2024-04-02T14:52:18.857ZE-MTAB-13984ERP159141EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0004184