READ ME File For 'Gene expression counts and differentially expressed genes'

Dataset DOI: 10.5258/SOTON/D3551

Date that the file was created: September, 2023

-------------------
GENERAL INFORMATION
-------------------

ReadMe Author: James Bedford, University of Southampton, ORCID ID 0000-0003-2471-8757

This dataset supports the thesis entitled Genomics of Local Adaptation in Wild Rice
AWARDED BY: Univeristy of Southampton
DATE OF AWARD: 2025

DESCRIPTION OF THE DATA
Gene expression count data generated for 13 wild rice accessions (Oryza rufipogon) under control and drought treatments across four populations, and the resulting lists of differentially expressed genes.

This dataset contains:
Chapter_4_Gene_expression_counts.txt	Gene expression count data from 13 wild rice accession from four population groups following control and drought treatments. Counts generated with the software RSEM version 1.3.3. 
Chapter_4_Differentially_expressed_genes.xlsx	List of differentially expressed genes across seven tables
- Table 1 - Genes significantly upregulated between control and drought stress treatments.
- Table 2 - Genes significantly downregulated between control and drought stress treatments.
- Table 3 - Genes significantly upregulated between control and drought stress treatments per population group.
- Table 4 - Genes significantly downregulated between control and drought stress treatments per population group.
- Table 5 - Genes significantly differentially expressed between populations under control conditions.	
- Table 6 - Genes significantly differentially expressed between populations under drought conditions.
- Table 7 - Genes significantly differentially expressed as the interaction between population group and treatment.

Relationship between files, if important for context: Chapter_4_Differentially_expressed_genes.xlsx is derived from analysis of Chapter_4_Gene_expression_counts.txt with the R package DESeq2.   

Date of data collection: August 2023

Related projects/Funders:
INSPIRE DTP NE/S0007210/1

--------------------------
SHARING/ACCESS INFORMATION
-------------------------- 

Licence:
CC BY

Recommended citation for the data:

This dataset supports the thesis:
Bedford, J.A. (2025) "Genomics of Local Adaptation in Wild Rice", University of Southampton, School of Ocean and Earth Science, PhD Thesis, p87-107