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Series GSE312411 Query DataSets for GSE312411
Status Public on Dec 30, 2025
Title RNAseq analysis of Sorghum under nitrate limitation and recovery at different time points.
Organism Sorghum bicolor
Experiment type Expression profiling by high throughput sequencing
Summary Nitrogen availability strongly influences sorghum growth, physiology, and yield, making enhanced nitrogen use efficiency (NUE) critical for agricultural sustainability. To characterize transcriptional responses to nitrate availability in sorghum, we profiled genome-wide gene expression changes under nitrate-sufficient, nitrate-limiting, and nitrate-recovery conditions. This dataset provides temporal resolution of nitrate-responsive regulation in roots and leaves, enabling comparative insights into nitrogen signaling and assimilation.
 
Overall design Sorghum (Sorghum bicolor, genotype BTx623, v3.1.1 reference genome) seeds were germinated on rag dolls and transferred to hydroponic tanks containing full-strength Hoagland nutrient solution at 10 days after germination (10 DAG). After 12 days under nitrate-sufficient conditions, plants at the 5th leaf stage (21 DAG) were transferred to a nitrate-limiting nutrient solution in which Ca(NO₃)₂ and Mg(NO₃)₂ were replaced with CaCl₂ and MgSO₄. Root and leaf tissues were harvested at the following time points under nitrate limitation: 0 min (baseline), 30 min, 3 hours, and 24 hours (1 day). After 24 hours of nitrate deprivation, nitrate was added back to the nutrient solution. Recovery samples were collected at: 24 h + 30 min and 24 h + 48 h (2 days). Three biological replicates were collected per tissue and treatment, with each replicate consisting of pooled tissue from five plants. RNA-seq libraries were prepared using the NEBNext RNA-seq Library Prep Kit and sequenced on the Illumina NextSeq 2000. Reads were processed with Trimmomatic, aligned to the Sorghum bicolor BTx623 v3.1.1 genome using STAR, and quantified with StringTie. Differential expression analysis was performed using DESeq2.
 
Contributor(s) Kumari S, Braynen J, Zhang L, Reguski M, Olson A
Citation(s) 41411658
BioProject PRJNA883413
Submission date Dec 03, 2025
Last update date Dec 30, 2025
Contact name Sunita Kumari
E-mail(s) r2sunita@gmail.com
Organization name Cold Spring Harbor Lab
Street address One Bungtown Road
City Cold Spring Harbor
State/province New York
ZIP/Postal code 11724
Country USA
 
Platforms (1)
GPL27913 Illumina HiSeq 4000 (Sorghum bicolor)
Samples (63)
GSM9345326 RNA-seq of sorghum bicolor: T0h Leaves 1-NN
GSM9345327 RNA-seq of sorghum bicolor: T0h Leaves 2-NN
GSM9345328 RNA-seq of sorghum bicolor: T0h Leaves 3 -NN

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE312411_Expression_TPM_Lateral-Roots-sorghum.csv.gz 2.7 Mb (ftp)(http) CSV
GSE312411_Expression_TPM_Primary-Roots-sorghum.csv.gz 2.6 Mb (ftp)(http) CSV
GSE312411_Expression_TPM_leaves-sorghum.csv.gz 2.5 Mb (ftp)(http) CSV
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Raw data are available in SRA

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