{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Eui-Jung Kim"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Oryza sativa Japonica Group"],"species":["Oryza sativa Japonica Group"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13984"],"description":["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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Yu-Jin Kim","Eui-Jung Kim","Ye-jin Son","Ki-Hong Jung"],"additional_accession":[]},"is_claimable":false,"name":"RNA sequencing of control and OsPRK1/2/3 triple knockout mutant in mature rice anthers (Oryza sativa japonica)","description":"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.","dates":{"release":"2025-07-14T00:00:00Z","modification":"2025-07-02T12:01:08.797Z","creation":"2024-04-02T14:52:18.857Z"},"accession":"E-MTAB-13984","cross_references":{"ENA":["ERP159141"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"]}}