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

PRJNA237453: Sorghum nitrogen stress tolerance

Source: NCBI / GSE54705
Submission Date: Feb 05 2014
Release Date: May 01 2014
Update Date: May 15 2019

Summary: Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).

Overall Design: RNAseq deep sequencing

GEN Datasets:
GEND000282
Strategy:
Species:
Tissue:
Isolation_source:
Development Stage:
Protocol
Growth Protocol: The seeds were grown in three inch pots under a 16/8 h photoperiod at 25°C (day) and 18°C (night).
Treatment Protocol: No treatment
Extract Protocol: Total RNA was extracted first using NTES buffer (20 mM TRIS pH 8, 10 mM EDTA, 100 mM NaCl and 1% SDS) and followed by Trizol reagent (Invitrogen) using the manufacturer’s instructions.
Library Construction Protocol: RNA libraries were prepared from 4 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 - Set A (RS-122-2002) according to the manufacturer’s instructions. Libraries were analyzed and measured by gel electrophoresis and NanoDrop 1000 Spectrophotometer to a concentration of 10 nM each. Four indexed libraries were pooled into one lane and clusters generated at 8 pM concentration were sequenced on the Illumina Genome Analyzer IIx (GAIIx; Illumina, Inc., San Diego, CA) using three 36-cycle sequencing kits to read 76 nucleotides of sequence from a single end of each insert, by standard multiplexing v8.3 protocol.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: SINGLE
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina Genome Analyzer IIx
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Publications
Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling.
BMC genomics . 2014-03-05 [PMID: 24597475]