Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

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A data portal of transcriptome profiles across multiple species
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PRJNA681502

PRJNA681502: The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions [RNA-seq]

Source: NCBI / GSE162311
Submission Date: Nov 30 2020
Release Date: Mar 07 2021
Update Date: Oct 15 2024

Summary: Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.

Overall Design: RNA-seq from root tips and leaves of 61 highly diversified rice accessions grown in the upland field.

GEN Datasets:
GEND000616
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: Sixty one accessions were cultivated at an upland field of the Institute of Crop Science (National Agriculture and Food Research Organization, Ibaraki, Japan; 36°02′89″ N and 140°09′97″ E), on a volcanic ash soil of the Kanto loam type (Humic Andosol) in 2018. Fertilizer of 5.2 g N m–2, 15.4 g P2O5 m–2, and 5.6 g K2O m–2 was supplied before rice planting.
Treatment Protocol: -
Extract Protocol: Total RNA was extracted by the HighGI method (Yoshino et al., Breeding Science 2020).
Library Construction Protocol: Equal amounts of RNA extracted from three independent plants were pooled, then RNA-seq libraries were prepared using NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs) following manufacturer's instruction.
Sequencing
Molecule Type: Poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NovaSeq 6169; Illumina NovaSeq 6170; Illumina NovaSeq 6171; Illumina NovaSeq 6172; Illumina NovaSeq 6173; Illumina NovaSeq 6174; Illumina NovaSeq 6175; Illumina NovaSeq 6176; Illumina NovaSeq 6177; Illumina NovaSeq 6178; Illumina NovaSeq 6179; Illumina NovaSeq 6180; Illumina NovaSeq 6181; Illumina NovaSeq 6182; Illumina NovaSeq 6183; Illumina NovaSeq 6184; Illumina NovaSeq 6185; Illumina NovaSeq 6186; Illumina NovaSeq 6187; Illumina NovaSeq 6188; Illumina NovaSeq 6189; Illumina NovaSeq 6190; Illumina NovaSeq 6191; Illumina NovaSeq 6192; Illumina NovaSeq 6193; Illumina NovaSeq 6194; Illumina NovaSeq 6195; Illumina NovaSeq 6196; Illumina NovaSeq 6197; Illumina NovaSeq 6198; Illumina NovaSeq 6199; Illumina NovaSeq 6200; Illumina NovaSeq 6201; Illumina NovaSeq 6202; Illumina NovaSeq 6203; Illumina NovaSeq 6204; Illumina NovaSeq 6205; Illumina NovaSeq 6206; Illumina NovaSeq 6207; Illumina NovaSeq 6208; Illumina NovaSeq 6209; Illumina NovaSeq 6210; Illumina NovaSeq 6211; Illumina NovaSeq 6212; Illumina NovaSeq 6213; Illumina NovaSeq 6214; Illumina NovaSeq 6215; Illumina NovaSeq 6216; Illumina NovaSeq 6217; Illumina NovaSeq 6218; Illumina NovaSeq 6219; Illumina NovaSeq 6220; Illumina NovaSeq 6221; Illumina NovaSeq 6222; Illumina NovaSeq 6223; Illumina NovaSeq 6224; Illumina NovaSeq 6225; Illumina NovaSeq 6226; Illumina NovaSeq 6227; Illumina NovaSeq 6228; Illumina NovaSeq 6229; Illumina NovaSeq 6230; Illumina NovaSeq 6231; Illumina NovaSeq 6232; Illumina NovaSeq 6233; Illumina NovaSeq 6234; Illumina NovaSeq 6235; Illumina NovaSeq 6236; Illumina NovaSeq 6237; Illumina NovaSeq 6238; Illumina NovaSeq 6239; Illumina NovaSeq 6240; Illumina NovaSeq 6241; Illumina NovaSeq 6242; Illumina NovaSeq 6243; Illumina NovaSeq 6244; Illumina NovaSeq 6245; Illumina NovaSeq 6246; Illumina NovaSeq 6247; Illumina NovaSeq 6248; Illumina NovaSeq 6249; Illumina NovaSeq 6250; Illumina NovaSeq 6251; Illumina NovaSeq 6252; Illumina NovaSeq 6253; Illumina NovaSeq 6254; Illumina NovaSeq 6255; Illumina NovaSeq 6256; Illumina NovaSeq 6257; Illumina NovaSeq 6258; Illumina NovaSeq 6259; Illumina NovaSeq 6260; Illumina NovaSeq 6261; Illumina NovaSeq 6262; Illumina NovaSeq 6263; Illumina NovaSeq 6264; Illumina NovaSeq 6265; Illumina NovaSeq 6266; Illumina NovaSeq 6267; Illumina NovaSeq 6268; Illumina NovaSeq 6269; Illumina NovaSeq 6270; Illumina NovaSeq 6271; Illumina NovaSeq 6272; Illumina NovaSeq 6273; Illumina NovaSeq 6274; Illumina NovaSeq 6275; Illumina NovaSeq 6276; Illumina NovaSeq 6277; Illumina NovaSeq 6278; Illumina NovaSeq 6279; Illumina NovaSeq 6280; Illumina NovaSeq 6281; Illumina NovaSeq 6282; Illumina NovaSeq 6283; Illumina NovaSeq 6284; Illumina NovaSeq 6285; Illumina NovaSeq 6286; Illumina NovaSeq 6287; Illumina NovaSeq 6288; Illumina NovaSeq 6289; Illumina NovaSeq 6290
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Condition Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate