Similar Datasets
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression profiles of a chlorosis mutant of Pakchoi. The goals of this study are to transcriptome analysis of a chlorosis. Methods: mRNA profiles of the aboveground parts of WT and a chlorosis mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://brassicadb.org/brad/index.php, v1.5）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays. Results: Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2958 DEGs was identified. Among 2958 DEGs, 9 DEGs related to chlorophyll synthesis and chlorophyll metabolism were identified. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular mechanisms of leaf color mutant. Conclusions: The results presented here reveal changes in the transcriptome profile of a chlorosis mutant. DEGs related to chlorophyll biosynthesis were detected.. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.
2019-03-23 | GSE112255 | GEO
Project description:Elevated CO2 (eCO2) has an influence on developing leaf growth of rice (Oryza sativa cv. Nipponbare), specifically lower growth stage than P4 (plastochron number), resulting in decrease in leaf size compared with that in ambient CO2 (aCO2). Since several micro RNAs are associated with the regulation of plant leaf development, in order to clarify which micro RNAs are involved in the decrease of leaf blade size at eCO2, we carried out high-throughput small RNA sequencing analysis and compared the amount of identified miRNAs in developing rice leaf blade grown between aCO2 and eCO2 condition.
2022-04-06 | GSE186906 | GEO
Project description:To investigate the genome-wide occupancies of INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), IBH1 ChIP analysis followed by direct sequencing (ChIP-Seq) on the p35S::IBH1-GFP (IBH1OE) line and a control line p35S::GFP (GFP OE) were conducted. Antibodies against GFP in the GFP-tagged IBH1 were utilized for immunoprecipitation of the endogenous protein-DNA complex, and the obtained DNA was subjected to next generation sequencing. Observation of genome-wide occupancies of atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060)
2014-03-05 | E-GEOD-51120 | biostudies-arrayexpress
Project description:Illumina-based whole genome bisulfite sequencing libraries for 4 RNA-directed DNA methylation mutants Examining DNA methylation levels in leaf tissue of RNA-directed DNA methylation mutants
2012-05-26 | E-GEOD-36143 | biostudies-arrayexpress
Project description:Senescence is the ultimate stage of plant development. Among the different levels of senescence processes, flag leaf senescence plays a crucial role in determining grain quality in rice. In the present study, efforts are made to identify the possible involvement of miRNAs in flag leaf senescence. Four small RNA libraries were generated from different stages of flag leaf senescence and sequenced by Illumina deep sequencing. A total of 29 known miRNA families and 494 novel miRNAs were identified in the senescing flag leaves. 21 known and 116 novel miRNAs exhibited differential expression pattern. Computational prediction and analysis of putative targets of detected miRNAs revealed that miRNAs regulate the flag leaf senescence mainly by regulating transcription factors and hormone metabolism genes. The present study gives a clue about the senescence-associated miRNAs which can be used as a tool for manipulating flag leaf senescence in rice and other crops.
2021-11-30 | GSE123171 | GEO
Project description:A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).
2018-07-28 | GSE111490 | GEO