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Oryza sativa Indica Group strain:Nagina 22

ABSTRACT: Oryza sativa ssp. Indica cv. Nagina 22 genome sequencing project

PROVIDER: PRJNA56083 | ENA |

REPOSITORIES: ENA

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Oryza sativa cultivar:Nagina 22

Project description:Oryza sativa cultivar:Nagina 22 Raw sequence reads

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Oryza sativa cultivar:Nagina 22

Project description:Oryza sativa cultivar:Nagina 22 Transcriptome or Gene expression

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ChIP-seq of Oryza sativa ssp. indica epilines

Project description:The contained data consist of Illumina NextSeq reads generated genomic DNA of Oryza sativa ssp. indica used for ChIP-seq analysis. The inbred control line and a derived epiline LR2 of the 5th selfing were analysed using chromatin immunoprecipitation sequencing.

2020-06-21 | E-MTAB-6982 | biostudies-arrayexpress

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Project description:de novo genome assembly of Oryza sativa ssp. indica cv. IR64

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Project description:The contained data consist of Illumina HiSeq reads generated genomic RNA of Oryza sativa ssp. indica used for RNA-seq analysis. The inbred control line and derived epilines LR1, LR2 and LR3 of the 4th selfing were analysed using RNA-seq.

2020-03-04 | E-MTAB-6983 | biostudies-arrayexpress

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced

2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress

Oryza sativa ssp. indica Illumina lwhole-genome bisulfite sequencing used for coverage comparison next to the method plant-RRBS

Project description:The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for comparative coverage aspects with plant-RRBS methylome profiling by bioinformatics analyses. The inbred control line and a derived epiline LR2 of the 4th selfing were analysed using whole-genome bisulfite sequencing.

2017-12-14 | E-MTAB-5002 | biostudies-arrayexpress

Salt stress in salt sensitive Oryza sativa Indica group IR29

Project description:Oryza sativa Indica group IR29 (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 24 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.

2017-10-02 | E-MTAB-1913 | biostudies-arrayexpress

Illumina whole-genome bisulfite sequencing of Oryza sativa ssp. indica inbred control and epilines

Project description:The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for WGBS analysis. The inbred control line and derived epilines LR1, LR2 and LR3 of the 4th selfing were analysed using whole-genome bisulfite sequencing. Control and LR2 lines can be found in ArrayExpress E-MTAB-5002 submission, LR1 and LR3 are part of this submission

2020-06-21 | E-MTAB-6981 | biostudies-arrayexpress

Oryza sativa ssp. indica Illumina libraries of the method plant-RRBS used for methylome profiling

Project description:The contained data consist of Illumina HiSeq 2500 reads generated from restriction endonuclease digested genomic DNA of Oryza sativa ssp. indica used as proof of concept for plant-RRBS methylome profiling by bioinformatics analyses. Five biological repeats for an inbred control line and a derived epiline of the 4th generation where analysed using two restriction endonuclease combination (MspI-DpnII or MspI-ApekI).

2017-12-14 | E-MTAB-4626 | biostudies-arrayexpress

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