TMT quantitative proteomics between WT and erf34 mutant Arabidopsis seedings after 100μM ABA treatment for 3 hours
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ABSTRACT:
ORGANISM(S): Arabidopsis Thaliana
SUBMITTER: 
Zecheng Zuo
PROVIDER: PXD048420 | iProX | Tue Jan 09 00:00:00 GMT 2024
REPOSITORIES: iProX
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Project description:After seven days of cultivation under continuous light on 1/2 MS medium, Arabidopsis thaliana seedlings were subjected to a 3-hour dark treatment in liquid 1/2 MS medium. Subsequently, they were transferred to 1/2 MS liquid medium supplemented with 100 μM ABA for 3h
2024-01-09 | PXD048436 |
Project description:Individual nucleotide crosslinking and immunoprecipitation (iCLIP2) of SR34a-GFP or control GFP from seeds germinated for 44 hours in continuous light and transferred to a control or ABA-containing medium during 2 hours.
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Project description:Transcriptome profiles of wild-type (WT) and sr34a-1 mutant seeds germinated for 44 hours in continuous light and transferred to a control or ABA-containing medium during 2 hours.
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Project description:Protein profiling of Arabidopsis thaliana seedling under nitrogen depreciation. Seven days old seedlings of Aradidopsis thaliana were transferred to nitrogen depreciated MS medium for further 48 hours cultivation. Same number of seedlings received same treatment except using MS medium were acted as control. After treatment, whole seedlings were extracted for protein profiling study.
2018-11-21 | PXD007190 | Pride
Project description:In Arabidopsis thaliana, four different DICER-LIKE (DCL) proteins have distinct, but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from longer, non-coding precursor RNAs. To analyze the impact of different components of the small RNA (sRNA) biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in sRNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. We discovered distinct effects of dcl1, hyl1 and se mutations on the transcriptome, as well as a number of common genes affected in dcl1 and dcl2 dcl3 dcl4 triple mutants. Our results furthermore suggest that the DCL1 is not only involved in miRNA action, but can also contribute to silencing of certain transposons, apparently through an effect on DNA methylation. Together, our findings contribute to the knowledge of both specialization and overlap between different RNA silencing pathways. Wild type and dcl1-100, se-3, hyl1-2, rdr6-15 ans dcl2,3,4 mutants were grown on MS or soil at 23M-BM-0C and LL. 7 day old seedlings (grown on MS plates) and inflorescences from 28 (>40) day old plants (dcl1) were used for RNA extraction. For stress treatments, seedlings had been grown for 10 days on solid MS medium at 21M-BM-0C, they were transferred to liquid MS medium containing no additives (mock control), 200 mM NaCl (salt stress), 300 mM mannitol (osmotic stress) or 100 M-NM-<M ABA. For cold and heat stress, seedlings were transferred to pre-chilled or pre-warmed liquid MS medium and incubated at 8M-BM-0C and 30M-BM-0C, respectively. Samples were taken after 1 h and 12 h of continuous stress treatment. RNA was extracted from whole seedlings. All RNA samples were converted into double stranded DNA targets that were hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). All hybridizations were performed with 3 biological replicates.
2010-05-07 | E-GEOD-21685 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. Candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
2023-01-01 | GSE193111 | GEO
Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, WT and sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. There are 6230 candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
2021-06-30 | GSE163057 | GEO
Project description:rs08-05_bac2 - bac2-catma - We are studying the function of a gene encoding a mitochondrial basic amino acid carrier , BAC2 in Arabdopsis thaliana.This gene is expressed during osmotic and salt stresses, and dark-induced senescence. We wish to determine whether there are transcriptome modifications during osmotic stress in mutant plants (bac2) compared to wild-type plants . - Mutant and Wild-type plants were grown on grids for 7 days on plates containing MS/2 and saccharose. Plants were transferred for 24h to liquid medium containing MS/2 saccharose (untreated plants) or 0.4M mannitol MS/2 saccharose (treated plants). Keywords: gene knock out,treated vs untreated comparison,wt vs mutant comparison
2009-10-01 | GSE15063 | GEO
Project description:Arabidopsis thaliana seeds after imbibition were inoculated in ½ MS medium supplemented with 0.8% agar and 1% sucrose. Once the plant material was uniformly germinated, the experimental conditions were applied. 5d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by ½ MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ½ MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22oC for 24 h and then 3 h treatment was given with liquid ½ MS without glucose and liquid ½ MS supplemented with BR (0.1 ?M EBR), glucose (3%), glucose (3%) + BR (0.1 ?M EBR). Seedlings were harvested after 3h and preceded for RNA isolation and Microarray analysis.
2011-05-18 | E-MEXP-2714 | biostudies-arrayexpress
Project description:imbibed Col-0 seeds were sown on ? X MS medium supplemented with 0.8% agar and 1% sucrose. The plates were first exposed to continuous light for 12 h to stimulate germination and then wrapped with two layers of aluminum foil and placed in the growth chamber for 5 d. Once the plant material was uniformly germinated, the experimental conditions were applied. 5-d-old, dark-grown seedlings were washed seven times with sterile water followed by a wash with ? X MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ? X MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22 C for 24 h and then treated with ? X MS without glucose or ½ X MS supplemented with BR (100 nM), glucose (3%), or glucose (3%) + BR (100 nM) for 3 h. Seedlings were harvested after 3h and preceded for RNA isolation and microarray analysis.
2012-08-10 | E-MEXP-3545 | biostudies-arrayexpress