45-day-leaf tissue of the above-mentioned materials was used to examine the effect of aneuploidy and polyploidy on miRNA expression through sRNA-seq. In addition, analysis of W22 diploid plants with one B chromosome (1B) relative to plants without any B chromosome (0B) was used as a cont...
Here, using published RNA-Seq and small RNA-Seq (sRNA-Seq) data from maize anthers at ten developmental stages in three genic male-sterility (GMS) mutants (ocl4, mac1, and ms23) and wild type W23, as well as newly sequenced maize anther transcriptomes of ms7-6007 and lob30 GMS ...
For sRNA-seq data37, we first used Trimmomatic version 0.32 to remove the linker adapter sequences38. The trimmed reads were then mapped to version 4 of the B73 maize genome using Bowtie39. Read counts were normalized to 20 million to allow for the direct comparison across libraries. phasiR...
plots of 21-nt (n = 9), 22-nt (n = 212) and 24-nt (n = 6) small RNA (sRNA) clusters that are differentially expressed in WT andTPDpollen. The accumulation of ectopic 22-nt siRNAs occurs specifically inTPDpollen. log2fold change ≥ 2, FDR ≤ 0.01.e, Rep...
ChIP-seq: Chromatin immunoprecipitation sequencing CRISPR: Clustered regularly interspaced short palindromic repeats ER: Endoplasmic Reticulum GWAS: Genome-wide association study HSR: Heat stress response HSF: Heat shock factor HSP: Heat shock protein ...
DAP-seq analysis was conducted and reported in our previous study [29]. Peak analysis of promoter was carried out by IGV-sRNA [107, 108]. Centrality analysis of motifs The main motifs detected by DAP-seq were located in the peaks by the Homer software to acquire the motif position and ...
Notably, AGO18b-bound sRNAs showed a drastic decrease in the 24-nt population in both W22-ref and ago18b::mum tassels, accompanied by an increase of 21-nt sRNAs, as compared to their proportions in the sRNA-seq (Figs. 1b, 2b-c). In three of the four wild-type and mutant samples,...
Article Open access 14 June 2022 Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors Article Open access 09 October 2020 Prediction of plant complex traits via integration of multi-omics data Article Open access 10 August 2024 Data...
The mRNAseq was performed using the same samples used for the construction of the sRNA libraries. Validation of bioinformatics analysis by qRT-PCR The expression profiles of four Cu-miRNAs (miR397, miR398, miR408 and miR528) were assayed by stem–loop qRT-PCR [105, 106]. Total RNA ...
A total of 3183 genes are detected both in DAP-seq and RNA-seq data, potentially as the directly regulating genes of ZmMYC2. These genes are involved in various biological processes including plant growth and stress response. Besides the classiccis-elements like the G-box and E-box that ...