Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of Arabidopsis Thaliana siliques from WT (Col-0) and ZFP2-knockout mutant (zfp2-2)

ABSTRACT: This experiment seeks to elucidate the functional role of the ZFP2 transcription factor in Arabidopsis thaliana siliques via differential gene expression analysis. Total RNA extracted from pooled Arabidopsis siliques 12 days after flowering (DAF) was used for the assay, with 3 biological replicates each for WT and zfp2-2. For each sample, RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and sequenced with Illumina Novaseq-6000 using paired-end sequencing with read lengths of 150 base pairs at sequencing depths of ~ 2 million reads per sample.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Marek Mutwil

PROVIDER: E-MTAB-14605 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology and defective hormonal and stimulus responses. HY5 thus acts as an integrater that links various gene networks to coordinate plant development. Here we report an effort to experimentally map the HY5-mediated gene networks in Arabidopsis by integrating genomic loci occupied by HY5 and HY5-dependent gene expression profiles. Our results indicate HY5 binds to over 9,000 genes, which detectably impact the expression of over 1,100 genes, either positively or negatively. Further, HY5 indirectly regulates many other genes through sub-networks mediated by other regulators. In particular, we show that HY5 regulates eight microRNA (miRNA) genes, which in turn control transcript abundance of specific target genes. Over-expressing the HY5-targeted miR408 resulted in phenotypes that are opposite to hy5 mutants. Together our results revealed both the transcriptional and post-transcriptional components of the HY5-mediated gene networks responsible for the phenotypic complexity in plants. DNase I-treated total RNA was prepared from wild type and hy5-215 seedlings grown under wild type light (WL). The mRNA fraction was extracted from total RNA using Dynabeads oligo(dT)25 (Invitrogen) following the manufacturerM-bM-^@M-^Ys directions. First- and second-strand cDNA were generated usingSuperScript II and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the manufacturerM-bM-^@M-^Ys protocol (Illumina). Bowtie (Langmead et al., 2009) was used to map the sequence reads to the Arabidopsis genome and only uniquely mapped reads were used in subsequent analyses.

Dataset Information

RNA-seq of Arabidopsis Thaliana siliques from WT (Col-0) and ZFP2-knockout mutant (zfp2-2)

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets