Additional file 1: of Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes
Creators: name: Raheleh Mirdar Mansuri
name: Zahra-Sadat Shobbar
name: Nadali Babaeian Jelodar
name: Ghaffari, Mohammad
name: Ghorban-Ali Nematzadeh
name: Saeedeh Asari
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Table S1. Summary of sequencing results. Table S2. A summary of the assembly statistics. Table S4. Highly enriched gene ontology (GO) terms for the differentially expressed intron retention (IR). Table S5. List of primers used for qRT-PCR analysis. Figure S1. PCA analysis and the distributions of FPKM scores based on replicates. PCA of transcriptome data in FL478 (a) and IR29 (b). The cs Density plot based on the distributions of FPKM scores in FL478 (c) and IR29 (d). Figure S2. Grouping transcripts into annotated, un-annotated, and annotated and un-annotated novel transcripts in FL478 and IR29. Figure S3. GO term assignment of novel transcripts identified in IR29 and FL478 cultivars (BP: biological processes, MF: molecular function, CC: cellular component). Figure S4. GO classifications of (a) up-regulated and (b) down-regulated DEGs between FL478 and IR29. Figure S5. Transcription factor families differentially expressed in the rice cultivars under salt stresses. Figure S6. A visualized overview of the metabolic pathways in rice cultivars a) FL478 and b) IR29 under salt stress drown by MapMan. Color coding; red: up-regulated transcripts and blue: down-regulated transcripts.Figure S7. A graphical visualization of metabolic pathways involved in differentially expressed transcripts in a) FL478 and b) IR29 under salt stress drown by MapMan. Color coding; red: up-regulated transcripts and blue: down-regulated transcripts. Figure S8. Schematic overview of gene regulation of differentially expressed transcripts in rice cultivars under salinity stresses, as drawn by MapMan. Various pathways were enriched in FL478 rice cultivar under salinity stress (a) and IR29 rice cultivar under salinity stress (b). Color coding; red: up-regulated transcripts and blue: down-regulated transcripts. Figure S9. Differential expression of transcripts produced through intron retention (IR) event in FL478 and IR29. Figure S10. Geneontology enrichment statistics of transcripts produced through a) Exon skipping and b) Alternative donor in FL478 and IR29. (DOCX 3446 kb)