Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq GLV6 overexpression during lateral root initiation in Arabidopsis thaliana

ABSTRACT: The goal of this experiment was to identify the downstream targets of the GOLVEN6 peptide signaling pathway in Arabidopsis thaliana, specifically during lateral root initiation. Using an estradiol inducible GLV6 overexpression construct in wildtype and rgi1rgi5 double mutant (mutant in receptors for the GLV6 peptide) backgrounds, in combination with gravistimulation induced lateral root formation, the RGI receptor dependent transcriptional effects of GLV6 overexpression were characterized. An estradiol inducible GLV6 overexpression line in a wildtype (iGLV6) and in an rgi1rgi5 double receptor mutant background (rgi1rgi5/iGLV6) were used. 4-day old seedlings of both lines were gravistimulated (vertically grown seedlings were turned counterclockwise by 90°) to induce lateral root initiation in the resulting root bends. 8h after gravistimulation, seedlings of both lines were treated with 2µM of estradiol to induce GLV6 overexpression, or DMSO as a mock treatment. 3h and 6h after treatment, root bends were dissected and collected for RNA-sequencing. This yielded a total of 8 samples per replicate; 3h mock treated iGLV6 (IM3), 3h estradiol treated iGLV6 (IE3), 3h mock treated rgi1rgi5/iGLV6 (RM3), 3h estradiol treated rgi1rgi5/iGLV6 (RE3), 6h mock treated iGLV6 (IM6), 6h estradiol treated iGLV6 (IE6), 6h mock treated rgi1rgi5/iGLV6 (RM6), 6h estradiol treated rgi1rgi5/iGLV6 (RE6). For each sample, 4 replicates were obtained. This setup enabled the comparison of the GLV6 induced transcriptional effects between wildtype and rgi1rgi5 mutants at 2 time points after treatment, in samples that are strongly enriched for lateral root initiation events.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Boris Parizot

PROVIDER: E-MTAB-10891 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Two phylogenetically unrelated peptide-receptor modules jointly regulate lateral root initiation via a partially shared signaling pathway in Arabidopsis thaliana.

Jourquin Joris J Fernandez Ana Ibis AI Parizot Boris B Xu Ke K Grunewald Wim W Mamiya Akihito A Fukaki Hidehiro H Beeckman Tom T

The New phytologist 20220103 4

Peptide-receptor signaling is an important system for intercellular communication, regulating many developmental processes. A single process can be controlled by several distinct signaling peptides. However, since peptide-receptor modules are usually studied separately, their mechanistic interactions remain largely unexplored. Two phylogenetically unrelated peptide-receptor modules, GLV6/GLV10-RGI and TOLS2/PIP2-RLK7, independently described as inhibitors of lateral root initiation, show strikin ...[more]

PMID: 34913488

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Project description:Untreated or 20 J/m2 UVC treated RKO cells were collected and RNA from either whole-cell lysates or from polysomal fractions was extracted at 0 (untreated), 3, 6, and 12 h after treatment. RNA from whole-cell lysates or each of 11 polysomal fraction was reverse-transcribed in the presence of [α-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays. The experiment was repeated using three independent sample sets. The samples were named T-c-A, T-c-B, T-c-C, T-3h-A, T-3h-B, T-3h-C, T-6h-A, T-6h-B, T-6h-C, T-12h-A, T-12h-B, T-12h-C, P-c-1-A, P-c-2-A, P-c-3-A, P-c-4-A, P-c-5-A, P-c-6-A, P-c-7-A, P-c-8-A, P-c-9-A, P-c-10-A, P-c-11-A, P-c-1-B, P-c-2-B, P-c-3-B, P-c-4-B, P-c-5-B, P-c-6-B, P-c-7-B, P-c-8-B, P-c-9-B, P-c-10-B, P-c-11-B, P-c-2-C, P-c-3-C, P-c-4-C, P-c-5-C, P-c-6-C, P-c-7-C, P-c-8-C, P-c-9-C, P-c-10-C, P-c-11-C, P-3h-1-A, P-3h-2-A, P-3h-3-A, P-3h-4-A, P-3h-5-A, P-3h-6-A, P-3h-7-A, P-3h-8-A, P-3h-9-A, P-3h-10-A, P-3h-11-A, P-3h-1-B, P-3h-2-B, P-3h-3-B, P-3h-4-B, P-3h-5-B, P-3h-6-B, P-3h-7-B, P-3h-8-B, P-3h-9-B, P-3h-10-B, P-3h-11-B, P-3h-1-C, P-3h-2-C, P-3h-3-C, P-3h-4-C, P-3h-6-C, P-3h-7-C, P-3h-8-C, P-3h-9-C, P-3h-10-C, P-3h-11-C, P-6h-1-A, P-6h-2-A, P-6h-3-A, P-6h-4-A, P-6h-5-A, P-6h-6-A, P-6h-7-A, P-6h-8-A, P-6h-9-A, P-6h-10-A, P-6h-11-A, P-6h-1-B, P-6h-2-B, P-6h-3-B, P-6h-4-B, P-6h-5-B, P-6h-6-B, P-6h-7-B, P-6h-8-B, P-6h-9-B, P-6h-10-B, P-6h-11-B, P-6h-1-C, P-6h-2-C, P-6h-3-C, P-6h-4-C, P-6h-5-C, P-6h-6-C, P-6h-7-C, P-6h-8-C, P-6h-9-C, P-6h-10-C, P-6h-11-C, P-12h-1-A, P-12h-2-A, P-12h-3-A, P-12h-4-A, P-12h-5-A, P-12h-6-A, P-12h-7-A, P-12h-8-A, P-12h-9-A, P-12h-10-A, P-12h-11-A, P-12h-1-B, P-12h-2-B, P-12h-3-B, P-12h-4-B, P-12h-5-B, P-12h-6-B, P-12h-7-B, P-12h-8-B, P-12h-9-B, P-12h-10-B, P-12h-11-B, P-12h-1-C, P-12h-2-C, P-12h-3-C, P-12h-6-C, P-12h-7-C, P-12h-8-C, P-12h-9-C, P-12h-10-C, P-12h-11-C. ‘T’ represents total RNA, ‘P’ represents RNA from polysomes fractions, ‘c’ represents RNA from untreated cells, ‘3h’ represents RNA from cells collected 3 h after UVC treatment, ‘6h’ represents RNA from cells collected 6 h after UVC treatment, ‘12h’ represents RNA from cells collected 12 h after UVC treatment. The numbers 1-11 correspond to the each polysomal fraction. The letters A, B and C correspond to the three independent experimental datasets. Keywords = post-transcriptional / translation / nascent protein synthesis / stress response / ribonomics Keywords: ordered

Dataset Information

RNA-seq GLV6 overexpression during lateral root initiation in Arabidopsis thaliana

Publications

Two phylogenetically unrelated peptide-receptor modules jointly regulate lateral root initiation via a partially shared signaling pathway in Arabidopsis thaliana.

Similar Datasets

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