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

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJCA000470: dynamic RNA-Seq of rice shoot gravitropism

Source: NGDC / CRA000335
Submission Date: May 17 2017
Release Date: Jul 16 2018
Update Date: -

Summary: Exploring regulatory mechanism of rice tiller angle through dynamic transcriptome of shoot gravitropism

GEN Datasets:
GEND000311
Strategy:
Species:
Tissue:
Height/Length/Weight:
Isolation_source:
Protocol
Growth Protocol: For RNA-seq and time-lapse photography, germinated ZH11 seeds were grown on 0.4% (w/v) agar plates at 28°C for 3 d under a 16-h-light/8-h-dark photoperiod, and then seedlings with uniform growth were transferred into soil and grown under controlled greenhouse conditions (16 h light and 8 h dark at 28°C, 150-200 μmol photons m-2 s-1) for 11 d prior to the gravistimulation treatments.
Treatment Protocol: Shoot bases (1.5 cm in length) were harvested at 12 time points (0, 0.25, 0.5, 1, 1.5, 2, 3, 4, 5, 6, 7, and 8 h) after the start of gravistimulation and were frozen immediately in liquid nitrogen.
Extract Protocol: RNA was extracted using a TRIzol kit according to the user manual (Invitrogen).
Library Construction Protocol: Illumina Part #15026495 Rev.D
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: Single
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2000
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
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 Case Detail Control 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
Publications
A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin.
The Plant cell . 2018-06-18 [PMID: 29915152]