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Next generation sequencing facilitates quantitative analysis of wild type and overexpression of PuC3H35 transgenic lines Transcriptomes

ABSTRACT: For the RNA-seq experiments there week-old seedlings were cutting and subsequently transfer to 1/2 MS medium with or without 6% PEG6000 for 7 d and harvested roots. Samples were collected from there biological replicates (12 seedings each).

ORGANISM(S): Populus ussuriensis

PROVIDER: GSE171096 | GEO | 2024/03/01

REPOSITORIES: GEO

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RNA-Seq timeseries of Adventitious root development in Populus ussuriensis

Project description:For the RNA-seq experiments two week-old seedlings were cutting and subsequently transfer to 1/2 MS medium with or without 1 μM MeJA at 2 time points over a 1-h period and harvested the basal ends of stem cuttings (0.5 cm). Samples were collected from two biological replicates (40 cuttings each).

2020-07-24 | GSE117619 | GEO

Next generation sequencing facilitates quantitative analysis of transcriptomes of wild type and overexpression of PuHSFA4a transgenic lines

Project description:Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between overexpression of PuHSFA4a transgenic lines and Wild Type with or without excess Zn stress Methods: Illumina HiSeq technology was used to generate mRNA profiles from PuHSFA4a transgenic roots compared to wild type roots.overexpression of PuHSFA4a and wild type material was obtained from root of Populus ussuriensis grown for 7 days in 1/2 MS medium only then exposed to 1/2 MS medium supplemented with 1.2mM ZnSO4 for two weeks. The control was plant grown for three weeks in 1/2 MS medium. Reads of 150bp were generated and aligned to the Populus trichocarpa reference genome (https://phytozome.jgi.doe.gov/pz/portal.html). qRT–PCR validation was performed using TransStart 1 Top Green qPCR SuperMix Results: By pairwise comparisons of the RNA-seq data, 33 genes were showed significant expression differences between PuHSFA4a-OE and WT (FDR adjusted P value < 0.01 including 17 genes under normal condition, 19 genes under excess Zn treatment. Altered expression of 17 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the detailed analysis of excess Zn response transcriptomes , with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that next generation sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2019-08-01 | GSE117778 | GEO

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Project description:Plant cyclophilins are widely involved in a variety of abiotic stress regulation processes. Thirty cyclophilin members were identified from apple and their patterns of response to abiotic stress were examined. Apple seedlings with consistent growth were selected, cultivated under drought stress conditions simulated by PEG6000, sampled according to different time periods, and quickly frozen in liquid nitrogen.Total RNAs of apple plantlets were isolated using an RNA extraction kit (Tiangen, Beijing, China).

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Differential gene expression in seedlings of pi4kb1b2-Study of pi4kb1b2 mutant

Project description:ngs2020_14_pi4kb1b2-differential gene expression in seedlings of pi4kb1b2-Differential gene expression in roots and leaves of seedlings, pi4kb1b2 mutant vs WT-Comparison of gene expression profile between roots and leaves of A.thaliana Col-0 as WT and pi4kb1b2 mutant, 7 days old (developmental stage 1.02), cultivated on MS/2 media supplemented with 0.8% agar and 1% sucrose, 22°C, 16h/8h light)

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Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment

Project description:Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates.

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AtSeedlingRootMunitionResponses

Project description:Roots transcriptome responses 14-day old Arabidopsis seedlings grown submerged in MS medium and exposed to TNT or RDX. Keywords = phytoremediation Keywords = explosives Keywords = TNT Keywords = RDX Keywords: parallel sample

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Transcription profiling of Arabidopsis roots with or without treatment with 9-hydroxyoctadecatrienoic acid

Project description:Gene expression of roots grown on MS medium versus MS+9HOT was compared. 6-day-old seedlings grown on MS were transferred to fresh plates and grown for 3- or 5- additional days in the absence or in the presence of 9-HOT (25 um). Root fragments grown after transferring to fresh plates were excised and used to compare gene expression between controls and 9-HOT treated seedlings.

2009-10-02 | E-ATMX-14 | biostudies-arrayexpress

Adventitious root formation in Populus trichocarpa involves complex cellular events

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Transcription profiling of Arabidopsis response to iron (Fe) deficiency - time series

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2008-06-11 | E-GEOD-10502 | biostudies-arrayexpress

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