Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5257973_1.fastq.gz | Fastqsanger.gz | |||
| SRR5257973_2.fastq.gz | Fastqsanger.gz | |||
| SRR5257974_1.fastq.gz | Fastqsanger.gz | |||
| SRR5257974_2.fastq.gz | Fastqsanger.gz | |||
| SRR5257975_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The douple mutant Arabidopsis thaliana soc1 ful, in contrast with WT, produces an interfascicular cambium and a large wood cylinder is the flowering stem. We present the RNAseq data for polyA mRNA of different developmental stages of cambium and wood formation in Arabidopsis thaliana. We sequenced 7 stages; 4 in the woody mutant soc1-6 ful-7 (herbaceous, cambium initiation, wood initiation and leaf) and 3 stages in the WT Col-0 (herbaceous, cambium and leaf). The corresponding stem anatomy is also presented in the manuscript indicating the stage of cambium development and the production of secondary xylem.
2016-05-21 | GSE69167 | GEO
Project description:In monocots other than the cereals maize and rice, the repertoire and diversity of microRNAs (miRNAs) and the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced small RNAs (sRNAs) from vegetative and dissected inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging angiosperm lineages, as well as publicly available data from 10 additional monocot species. We annotated miRNAs, siRNAs and phasiRNAs across the monocot phylogeny, identifying miRNAs apparently lost or gained in the grasses relative to other monocot families, as well as a number of tRNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these misannotations, we identified conservation at the 8th, 9th, 19th and 3’ end positions that we hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show that 21-nt reproductive phasiRNAs are far more numerous in grass genomes than other monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE 5 (DCL5), important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, siRNAs, and phasiRNAs is the largest collection to date, and should facilitate continued exploration of small RNA diversification in flowering plants.
2020-04-17 | GSE148762 | GEO
Project description:ChIP-seq was carried out with FLAG antibody using stem cambium tissues from PtrVCS2-FLAG overexpression plants
2022-11-11 | GSE201005 | GEO
Project description:Currently little is known about the genetic mechanisms regulating the vascular cambium or the secondary growth of stems. We show here that the Populus Class I KNOX homeobox gene ARBORKNOX2 (ARK2) regulates both cell division in the cambium region and the differentiation of daughter cells in secondary xylem and phloem. ARK2 is expressed in the shoot apical meristem, and the vascular cambium region, reflecting some overlap in the regulation of these meristems. ARK2 is expressed broadly in the cambium region and in differentiating lignified cells types before becoming progressively restricted to the cambium. Populus overexpressing ARK2 present stem phenotypes with precocious cambium formation, delayed differentiation of cambium daughter cells, a wider cambium region, and ultimately less phloem fibers and secondary xylem. In contrast, Populus expressing RNAi or amicroRNA that target ARK2 transcripts present precocious differentiation of secondary phloem fibers and xylem, and ultimately more secondary xylem tissue and thicker secondary cell walls in phloem fibers and secondary xylem cells. These phenotypes in turn correlate with changes in the expression of genes affecting cell division, auxin, and cell wall synthesis and lignification that indicate that ARK2 primarily affects woody tissue development by regulation of cell differentiation. Notably, wood properties associated with secondary cell wall synthesis are negatively associated with ARK2 expression, including lignin and cellulose content. Together, our results suggest that ARK2 functions primarily by negatively regulating cell differentiation during secondary growth. We propose that ARK2 may identify a co-evolved regulatory module that influences complex wood properties relevant to ecological, industrial, and biofuels applications.
2009-10-01 | GSE15595 | GEO
Project description:In-vitro induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under auxin treatments. We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium and identified tissue-speciffic up-regulated genes during this process. Different tissue types from in-vitro auxin treated stems were selected at successive stages of cambium establishment using laser capture microdissection for RNA extraction and hybridization on Affymetrix microarrays. We aimed to obtain genes exclussively upregulated in the interfascicular region responsible for cambium establishment and activity.
2010-12-31 | E-GEOD-22947 | biostudies-arrayexpress
Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer. Examination of mRNA levels in dormant, reactivating, and actively growing C. lanceolata vascular cambium, respectively
2014-03-31 | E-GEOD-37152 | biostudies-arrayexpress
Project description:In-vivo induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under NPA treatments. We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium.
2011-09-01 | GSE24763 | GEO
Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer.
2014-03-31 | GSE37152 | GEO
Project description:Wood is formed by the differentiation of cells from the vascular cambium and it is an important source for pulp, paper and bioenergy production. However there is little information about the vascular cambium at the molecular level, particularly in response to seasonality in tropical regions. We used three different molecular approaches: transcripts, proteome and metabolome to characterize the seasonal alterations in the primary metabolism of the eucalyptus cambial zone. Based on 2-DE analysis, 71 proteins were differentially expressed.
2016-07-26 | PXD003504 | Pride
Project description:Vascular cambium is a secondary meristem which produces xylem (wood) inwards and phloem (bark) outwards. The activity of cambium leads to expansion in the diameters in plants, that is, secondary growth, and thus contributes to biomass increase. The regulation of cambium development is at multilevel including phytohormones and peptide-receptor kinase (CLE41/44-PXY) signalling pathways. However, only limited progress has been made on the transcriptional regulation level. To construct the transcriptional network that regulates cambium development, we performed a genome wide transcript profiling in sorted procambial and cambial cells in Arabidopsis roots. More than 500 genes were identified as cambium abundant genes via comparison against transcriptomes of other Arabidopsis root cell types. We then investigated the roles of almost all the cambial transcription factors (TFs) and some of their homologous genes during secondary growth. Many of the candidate TFs were highly expressed in cambium based on the promoter GUS fusion and in situ hybridization. An unbiased transcriptional regulatory network was constructed using transcript profiling data collected from inducible overexpression lines for selected candidate TFs and a few major nodes were identified in the network including WOX4 and KNAT1. Moreover, the severity of mutant phenotypes was predicted based on the network. Next, we used the predication as a guide and generated over 70 double mutants within the same or among different TF families to explore the genetic interactions of candidate genes. Phenotype characterization on the secondary growth of the mutants and the overexpression lines identified promoters and inhibitors of cambium activity. The phenotypic data also suggested the redundancy within and among TF families because the phenotypes could be enhanced when additional TFs were mutated. We also found that combinations of certain overexpression lines and mutants led to pronounced increase of cell proliferation or xylem differentiation and in the extreme case the formation of ectopic cambium. We herein propose that cambium development is orchestrated by a wide network at the transcriptional level, where each TF has a different contribution to cell proliferation and differentiation.
2019-03-31 | GSE125244 | GEO