Table 1 List of NGS experiments, result tables and identifiers of inflorescence samples used in the current study.
From: Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX)-deficient Arabidopsis inflorescence
Data description | Tissue | Sample description | SRA/GEO reference | Data collection/Analytical step/Figure |
|---|---|---|---|---|
mRNA-seq (fastq) | flower | Col-0 wt, rep1 | mRNA sequencing, 75 bp single-end reads; Fig. 2 | |
Col-0 wt, rep2 | ||||
ndx1-4 mt, rep1 | ||||
ndx1-4 mt, rep2 | ||||
mRNA coverage (bigwig) | flower | Col-0 wt, rep1 | HISAT2: alignment to TAIR10 reference; deepTools: RPKM normalized read coverage; | |
Col-0 wt, rep2 | ||||
ndx1-4 mt, rep1 | ||||
ndx1-4 mt, rep2 | ||||
differentially expressed genes (tsv) | flower | ndx1-4 vs Col-0 | Salmon: quantification with GC bias correction; DESeq2: differential gene expression analysis, adjusted p-value < 0.01; data: counts, FPKM, log2FC, p-value (adjusted); Fig. 3 | |
differentially expressed transposable elements (tsv) | flower | ndx1-4 vs Col-0 | Salmon: quantification with GC bias correction, keeping duplicates; DESeq2: differential transposable element expres- sion analysis, adjusted p-value < 0.05; data: counts, FPKM, log2FC, p-value (adjusted) | |
sRNA-seq (fastq) | flower | Col-0 wt, rep1 | sRNA sequencing, 50 bp single-end reads; Figure 6 | |
Col-0 wt, rep2 | ||||
Col-0 wt, rep3 | ||||
ndx1-4 mt, rep1 | ||||
ndx1-4 mt, rep2 | ||||
ndx1-4 mt, rep3 | ||||
sRNA coverage (bigwig) | flower | Col-0 wt, rep1 | bowtie2: alignment to TAIR10 reference; deepTools: RPKM normalized read coverage; | |
Col-0 wt, rep2 | ||||
Col-0 wt, rep3 | ||||
ndx1-4 mt, rep1 | ||||
ndx1-4 mt, rep2 | ||||
ndx1-4 mt, rep3 | ||||
differentially expressed sRNAs (tsv) | flower | ndx1-4 vs Col-0 | DESeq2: differential sRNA expression analysis, adjusted p-value < 0.05; data: counts, log2FC, p-value (adjusted); Fig. 7 (cutoff: abs(FC) > 1.5) |
