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

PRJNA340947: Characterize novel lncRNAs responding to stresses in Oryza sativa at transcriptional and post-transcriptional levels

Source: NCBI / GSE86215
Submission Date: Aug 30 2016
Release Date: Jun 13 2018
Update Date: May 15 2019

Summary: We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.

Overall Design: We treated the seedlings under the stress conditions, including cold, drought, heat, high-salt, and high-light. Also, we choose two tissues, roots and panicles for RNA sequencing.

GEN Datasets:
GEND000258
Strategy:
Species:
Tissue:
Development Stage:
Protocol
Growth Protocol: We plant the Oryza sativa japonica on the ½ MS medium in a growth chamber under conditions of 12 hours light at 28℃ and 12 hours dark at 22℃ for 2 weeks.
Treatment Protocol: Drought, high-salt, cold, heat, highlight stress treatment.
Extract Protocol: The total RNAs were extracted with the Trizol reagent (Invitrogen). After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN).
Library Construction Protocol: dUTP based strand-specific library construction protocol
Sequencing
Molecule Type: poly(A)- RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2000; Illumina HiSeq 2500
Strand-Specific: Specific
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
Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa.
The Plant journal : for cell and molecular biology . 2018-01-16 [PMID: 29265542]