Arabidopsis RNA-Seq Data SetJason S CumbieJeff H Chang
An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level. bioinformaticsrna-seqdatabasedata-visualizationwebappalternative-splicingbamarabidopsisefprna-seq-mappingarabidopsis-th...
Data availability The RNA-seq raw sequencing and analysed data have been deposited in the NCBI Gene Expression Omnibus database under accession GSE218961 and GSE218962. Raw source 16S rRNA gene sequences from this project are available in the Sequence Read Archive database under BioProject PRJNA977...
RNA-seq data were mapped to the Arabidopsis TAIR10 genome release using the bioinformatic pipeline of the illumina Base Space Sequence Hub. Genes with a q value < 0.05 and absolute log2 fold change > 1 were defined as differentially expressed genes. GO enrichment analysis was performed...
An update to database TraVA: organ-specific cold stress response in Arabidopsis thalianaCold stress, Arabidopsis thaliana, RNA-seq, Transcriptome map, Organ-specific stress responseBackground Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include ...
The RNA sequencing data have been archived in the Short Read Archive database of the National Center for Biotechnology Information under the accession No. PRJNA506033. The RNA-seq data were trimmed using Trimmomatic (v0.36) program and mapped against A. thaliana annotated genes (TAIR10_Araport11...
New tools in science such as genome sequencing, RNASeq, microarrays, and metabolomics have provided enormous new data resources. Researchers are increasingly challenged to keep up with the avalanche of data and often feel overwhelmed. Fortunately, there are powerful search tools available to ‘mine’...
Because RNA-Seq detects a broader range of transcripts than microarrays, which are limited to the probe set, any genes not found on the array were first filtered from the RNA-Seq data. Log2 fold changes of differentially expressed genes in both RNA-Seq and mircoarray data was then compared...
The RNA-Seq transcriptome data was validated by qRT-PCR analysis for 16 NO-responsive AtWRKYs involved in different processes, including AtWRKY48, involved in plant defense (Xing et al., 2008), AtWRKY33, involved in abiotic stress regulation (Davletova et al., 2005), AtWRKY62, involved ...
Since TAIR10, around two hundred Arabidopsis thaliana RNA-Seq studies have been published and deposited in NCBI SRA. In comparison to the EST data that provided the bulk of the TAIR10 annotation, the RNA-Seq data offer single-base resolution and more precise measurement of levels of ...