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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

Overexpression of subtilate4.13

Project description:mutant seedlings overexpressing subtilase4.13 were grown in MS medium during 10 days comparing with wild type

2020-02-25 | GSE142459 | GEO

Real-time quantitative PCR analysis of 30 apple cyclophilin genes under abiotic stress

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).

2022-09-24 | GSE214087 | GEO

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)

2022-05-04 | GSE179635 | GEO

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.

2017-09-15 | GSE98903 | GEO

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

2003-07-30 | GSE560 | GEO

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

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

Project description:We performed a time course analysis (TC data set) of the response of whole seedling roots to -Fe at 6 time points after transfer (3, 6, 12, 24, 48, and 72 hours). Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Experiment Overall Design: Seedlings were grown for 5 days before transfer to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no iron sulfate). Whole roots were harvested at 6 time points after the transfer.

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

Adventitious root formation in Populus trichocarpa involves complex cellular events

Project description:Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 ± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. Stem cross-sections showed intensely dividing cells forming root primordial. One to two days later the bark split and the organized sequence of cell division and differentiation steps in the primordium led to the establishment of the main root tissues, as well as the vascular connections of the incipient root with the pre-existing stem vasculature. Subsequently, the outgrowth and emergence of the adventitious root occurred. We refer to the dormant cutting as stage 0, the organizing primordium as stage 1, the primordium differentiation as stage 2. To examine changes in gene transcription associated with the development of adventitious roots, we monitored the transcript levels in differentiating primordia using microarrays. cDNA was prepared from replicate sets of P. trichocarpa rooted cuttings harvested at stages 0, 1 and 2.

2012-11-01 | GSE34096 | GEO

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