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
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PRJNA243371

PRJNA243371: Transcriptome profiling of various organs at different developmental stages in rice (single-end)

Source: NCBI / GSE56463
Submission Date: Apr 02, 2014
Release Date: Nov 25, 2015
Update Date: May 15, 2019

Summary: To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection.

Overall Design: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

GEN Datasets:
GEND000540
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
Treatment Protocol: -
Extract Protocol: RNA was extracted using the Qiagen RNeasy Plant Mini kit. Total RNA was treated with Turbo DNase I (Life Technologies AM2238) according to product specification. DNase I treated RNA was then applied again to an RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to the manufacturer’s instructions.
Library Construction Protocol: Sequencing libraries were prepared using the Illumina Stranded mRNA sample Prep kit, set A (RS-122-2101, Illumina Inc.) according to the manufacturer's instructions. The quality and size of cDNA libraries for sequencing were checked using the Agilent 2200 TapeStation system (Agilent Inc.). The libraries were sequenced for 100 cycles on HiseqTM 2500 (Illumina Inc.)
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: SINGLE
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
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