Study Info
INDA Accessions: INRP000099
INSDC Accessions: PRJEB66718, ERP151775
- Title: Genome-wide analysis of DNase hypersensitive sites in rice cultivars
- Data Type : Whole Genome Sequencing
- Descriptive Title: Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility in rice cultivars
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Organism:
Scientific Name(Taxon Id): Oryza sativa (4530) Common Name: Asian cultivated rice
Other Info
- Abstract: In this study, we employed DNase I hypersensitive assays followed by sequencing to identify the accessible chromatin regions under drought stress in a drought-sensitive and a drought-tolerant rice cultivar. The raw reads from all the samples were processed to remove adaptors and low-quality reads using NGS QC toolkit with default parameters. The filtered reads of each sample were mapped to the Nipponbare rice reference genome using BWA-MEM at default parameters. The mapped reads from DNase I digested samples were compared against their respective input control for the identification of DHSs by using MACS3 . The DHSs with at least two fold-change were considered as true positives. Further, the consensus DHSs between the biological replicates were identified using a Bioconductor package, Irreproducible Discovery Rate at default parameters and subsequently used for downstream analyses. Next, we identified differential DHSs between the two rice cultivars under control condition and within the rice cultivar under drought stress. The differential DHSs with at least two fold-change were considered to be significant and used for downstream analyses. The annotation to DHSs was assigned using gff file, such as promoter, transcription start site, exon, intron, transcription termination site and intergenic regions.
- Linked publications:
- Center Name: Mukesh Jain, School of Computational and Integrative Sciences, Jawaharlal Nehru University
- Number of Base(Total) Mbp: 0
- Size in bytes(Total): 40,881,807,714
- Number of sample:
- Number of Runs:
- Number of Sequences:
- Number of Assembly:
- Number of Variant files:
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