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Transcription profiling of Arabidopsis plants overexpressing SlHsfA3

ABSTRACT: In order to investigate the possible molecular mechanisms of SlHsfA3 function in plant growth and stress responses, we employed the RNA-seq approach to identify the genes with altered expression levels in the transgenic Arabidopsis overexpressing SlHsfA3. Processing of RNA samples on the Illumina HiSeq 2000 system yielded more than 24 million reads, each 100bp in length, encompassing 2.4Gb of sequence data for each sample which was then mapped to the reference genome. Quantitative analysis of RNA-seq data identified substantial variation in expression profiles among different genotypes, consistent with known functional differences. Transcript abundance obtained from RNA-seq data was indicated as RPKMs and therefore, Up- and down-regulated genes were determined by a greater than 2-fold change of normalized RPKMs in comparison analysis (35S:SlHsfA3 transgenic plants versus Col-0(WT) plants) in both over-expression lines: Q-value < 0.05. The statistical analysis identified a total of 181 differentially expressed genes between OE lines and Col-0(WT) at Q-value < 0.05, among which 114 (63%) were up-regulated and 67 (37%) were down-regulated with fold changes higher than 2.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE40388 | GEO | 2013/08/01

SECONDARY ACCESSION(S): PRJNA173828

REPOSITORIES: GEO

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Transcription profiling of Arabidopsis plants overexpressing SlHsfA3

Project description:In order to investigate the possible molecular mechanisms of SlHsfA3 function in plant growth and stress responses, we employed the RNA-seq approach to identify the genes with altered expression levels in the transgenic Arabidopsis overexpressing SlHsfA3. Processing of RNA samples on the Illumina HiSeq 2000 system yielded more than 24 million reads, each 100bp in length, encompassing 2.4Gb of sequence data for each sample which was then mapped to the reference genome. Quantitative analysis of RNA-seq data identified substantial variation in expression profiles among different genotypes, consistent with known functional differences. Transcript abundance obtained from RNA-seq data was indicated as RPKMs and therefore, Up- and down-regulated genes were determined by a greater than 2-fold change of normalized RPKMs in comparison analysis (35S:SlHsfA3 transgenic plants versus Col-0(WT) plants) in both over-expression lines: Q-value < 0.05. The statistical analysis identified a total of 181 differentially expressed genes between OE lines and Col-0(WT) at Q-value < 0.05, among which 114 (63%) were up-regulated and 67 (37%) were down-regulated with fold changes higher than 2. RNA-sequencing was carried out using two independent transgenic lines (35S:SlHsfA3-3 and 35S:SlHsfA3-6). Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial part of the 4-week-old seedlings of 35Spro:SlHsfA3 and Col-0 (WT) plants grown in parallel under unstressed conditions. Materials from 20 plants of each genotype were pooled for RNA isolation.

2013-08-01 | E-GEOD-40388 | biostudies-arrayexpress

Transcriptome Profiling of Two Separatively Reproduced Arabidopsis Lines

Project description:We profiled transcriptome of seedling samples derived from SALK Col-0 plants and a Col-0 plants reproduced in our lab for at least 10 generations. Using strand-specific RNA-seq analysis, we identified 32 genes were differentially expressed genes (fold-change > 2, DESeq2 P-value < 0.01), including 28 ones (88%) were up-regulated in the Col-0 plants reproduced in our lab. Of them, QUA-QUINE STARCH (QQS) ranked top 2 differentially expressed gene.

2017-06-01 | GSE71085 | GEO

Transformants of wheat GSK3/Shaggy-like kinase TaSK5 vs wild-type Col-0

Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison

2014-11-02 | GSE59556 | GEO

Transcriptome analysis of transgenic plants with ectopic expression (driven by 35S promoter) of At14a-Like1 (AFL1, At3g28270) YFP fusion protein.

Project description:Transcriptome analysis was used to identify genes differentially expressed in transgenic plants expressing At14a-Like1 (AFL1, At3g28270)) YFP fusion protein compared to wild type. Transcriptome analysis was performed using seedlings grown under either control conditions or low water potential stress with the objective of identifying genes associated with the increased growth caused by AFL1 overexpression under stress. The analysis identified 172 genes up-regulated and 525 genes down regulated in 35S:AFL1-YFP relative to wild type in control condtions. In the stress treatment 398 genes were up regulated and 722 down regulated in 35S:AFL1-YFP plants relative to wild type. The criteria used to identify up and down regulated genes was fold change greater than 1.5 and corrected p value M-bM-^IM-$0.05. Wild type (Col-0) or transgenic Arabidopsis thaliana seedlings were germinated on agar plates and after seven days of growth, seedlings were transferred either to fresh plates of control media or to low water potential (-1.2 MPa) stress plates. Samples were collected 10 h after transfer.

2014-10-17 | E-GEOD-62413 | biostudies-arrayexpress

Microarray analysis of Psm-induced transcriptome changes in the systemic leaves of Arabidopsis plants

Project description:The goal of the microarray was to compare the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced transcriptome changes in the systemic leaves of the wild-type Col-0, lecrk-VI.2-2, and bak1-5 plants. Results showed that local Psm inoculation induced dramatic transcriptional changes in Col-0, with 564 and 151 genes up- and down-regulated at least twofold with a low q value (≤ 0.05), respectively. However, only 55 and 26 genes in lecrk-VI.2-2 and 221 and 121 genes in bak1-5 were up- and down-regulated, respectively. The majority of the genes that were induced or suppressed twofold or more with a low q value (≤ 0.05) in Col-0 were induced or suppressed to a smaller extent in bak1-5 and the smallest extent in lecrk-VI.2-2. These results indicate that both lecrk-VI.2-2 and bak1-5 suppressed Psm-induced systemic signaling with the lecrk-VI.2-2 mutation having a stronger effect than bak1-5.

2019-10-29 | GSE121886 | GEO

Transgenic Arabidopsis expressing AtMYB23SRDX

Project description:Comparison of gene expression between wild type Arabidopsis ecotype Col-0 plants and transgenic Arabidopsis ecotype col-0 plants expressing AtMYB23SRDX. Keywords: other

2004-07-07 | GSE1544 | GEO

Transformants of wheat GSK3/Shaggy-like kinase TaSK5 vs wild-type Col-0

2014-11-02 | E-GEOD-59556 | biostudies-arrayexpress

RNA sequencing (RNA-seq) for identifing differentially expressed transcription factor genes during early plant growth

Project description:The purpose of this study is to identify differentially expressed transcription factor genes during early plant growth. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We used an optimized data analysis workflow, and mapped about 45 million sequence clean reads per sample to the Arabidopsis genome and identified 33,685 transcripts in 2 and 6 dpg (day post germination) old wild type plant (Col-0). Among them, there are 9321 genes differentially expresses from 2- and 6-d-old plants, and 479 differentially expresses transcription factor (TF) genes. Of these genes, 344 TF genes up regulated and 135 down regulated in 6-d-old plants compared with 2-d-old plants, with a fold change ≥2, ≤0.6 and p value <0.05. The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. This study will facilitate analysis related with developmental study in early plant growth stage.

2018-12-31 | GSE119325 | GEO

Transcriptome analysis using RNA sequencing conducted for wild type (Col-0) and a stable transgenic line with ectopic expression of AT3G11290 (35S:HIN1) under control conditions and after 96 hours at moderate low water potential stress (-0.7 MPa)

Project description:RNA sequencing was used to identify alternative splicing events and differentially expressed genes (DEG) in 35S:HIN1 stable transgenic line compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hours moderate severity low water potential (-0.7 MPa) treatment. RNA sequencing analysis found that overexpression of HIN1 in unstressed plants was sufficient to duplicate the effects of stress on nearly 40% of the genes where intron retention was normally suppressed by stress in wild type. Differentially expressed genes (DEGs) were also analyzed (P < 0.05 and fold change ≥ 1.5 used as cut off values for DEGs). Differentially expressed genes in 35S:HIN1has limited overlap of DEGs between 35S:HIN1and wild type. This indicated that HIN1 plays a lesser role in stress-regulated gene expression than in splicing regulation.

2019-10-01 | GSE127805 | GEO

ThERF1 regulates its target genes via binding a novel cis-acting element in response to salt stress

Project description:To reveal the regulatory network of ThERF1 in response to abiotic stress, we have employed an Agilent Arabidopsis gene expression microarray to study the expression profile changes between Wild-type and transgenic plants overexpressing ThERF1 under salt stress. A total of 154 and 307 differentially expressed genes with p-value < 0.05 and ≥ 2-fold change were significantly up- and down- regulated in ThERF1-transformed plants under salt stress treatment.

2014-05-21 | GSE57847 | GEO

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