Transcriptome analysis of Arabidopsis Root in response to cellooligomers (cellotriose)
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE198092 | GEO | 2022/09/20
REPOSITORIES: GEO
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Project description:Cellulose is the major polysaccharide in the primary and secondary cell wall. Its breakdown generates short-chain cellooligomers (COs) which induce Ca2+-dependent cell wall integrity (CWI) responses. Recently, a mutant (cork1) which did not respond to COs was identified. To find out the early phosphorylation events following CO perception, roots of the segregated wild-type and homozygous mutants (F2 generation from cork1-2 X AeqWT) were treated with 10 µM cellotriose or water for 0, 5 and 15 minutes. Phosphoproteome analyses identified early targets involved in signaling, the endoplasmatic recticulum/Golgi secretory pathway, cell wall repair and immune responses. The result identified protein targets of the novel CO-CORK1 pathway and shine light on the role of COs in CWI maintenance.
2022-09-23 | PXD033224 | Pride
Project description:During sexual reproduction half of the genetic material is deposited in gametes and a complete set of chromosomes is restored upon fertilisation. Reduction of the genetic information prior gametogenesis occurs in meiosis where crossovers (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it has been postulated that DNA hypermethylation is inhibitory to COs. Here by analysing meiotic recombination in mutant plants with hypomethylated DNA we observed unexpected and counterintuitive effects of the DNA methylation losses on COs distribution, further promoting recombination in the naturally hypomethylated euchromatic chromosome arms, while inhibiting it in heterochromatic regions encompassing centromeric and pericentromeric hypermethylated DNA. Importantly, the total number of COs was not affected, implying that the loss of DNA methylation only led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influenced recombination, namely whether this occurred directly in cis or indirectly in trans by changing expression of genes encoding recombination components, we analysed COs distribution in WT lines with randomly scattered and well mapped hypomethylated chromosomal segments. Results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. As DNA methylation is subjected to significant variation even within a single species, our results implicate that it could influence evolution of plant genomes through the control of meiotic recombination. 2 samples: Col, epiRIL12, with 3 replicates each
2012-03-12 | E-GEOD-34173 | biostudies-arrayexpress
Project description:During sexual reproduction half of the genetic material is deposited in gametes and a complete set of chromosomes is restored upon fertilisation. Reduction of the genetic information prior gametogenesis occurs in meiosis where crossovers (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it has been postulated that DNA hypermethylation is inhibitory to COs. Here by analysing meiotic recombination in mutant plants with hypomethylated DNA we observed unexpected and counterintuitive effects of the DNA methylation losses on COs distribution, further promoting recombination in the naturally hypomethylated euchromatic chromosome arms, while inhibiting it in heterochromatic regions encompassing centromeric and pericentromeric hypermethylated DNA. Importantly, the total number of COs was not affected, implying that the loss of DNA methylation only led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influenced recombination, namely whether this occurred directly in cis or indirectly in trans by changing expression of genes encoding recombination components, we analysed COs distribution in WT lines with randomly scattered and well mapped hypomethylated chromosomal segments. Results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. As DNA methylation is subjected to significant variation even within a single species, our results implicate that it could influence evolution of plant genomes through the control of meiotic recombination.
2012-03-12 | GSE34173 | GEO
Project description:To identify differentially expressed mRNAs after knockdown of YTHDF2 in granule cells, we perfomed RNA-seq. Cultured granule cells were infected with lentiviral shYthdf2 or shCtrl. Total RNA was collected and subjected to construct sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB). After sequencencing, the filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. Differential expression analysis of two groups (shYthdf2 vs shCtrl) (three biological replicates per group) was performed using the DESeq R package (version 1.18.0). Altogether 923 mRNA were differentially regulated, among which 587 mRNA were upregulated after YTHDF2 KD. This study provides a gene list which shows differentially expressed mRNAs after knockdown of YTHDF2 in granule cells.
2021-12-10 | GSE153688 | GEO
Project description:To identify the target mRNAs of the m6A reader protein YTHDF2, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P0 wild type mouse retinas was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input and any fold change greater than 2 was considered enriched. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 1639 transcripts. This study provides a gene list which shows mRNA binding with YTHDF2 in mouse retina.
2022-03-15 | GSE145390 | GEO
Project description:To identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus, we perfromed RNA-seq. Total RNA from DG deficient in YTHDF2 and the negative control DG were collected and subjected to construct sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB). After sequencencing, the filtered reads were mapped to the mouse reference genome (GRCm38) using HISAT2 v2.0.5 with default parameters. The resulting bam files were fed to featureCounts v1.5.0-p3 to count the number of RNA-seq reads, which was further normalized to calculate FPKM. Differential expression analysis of two groups (cKO vs NC) (three biological replicates per group) was performed using the DESeq2 package (version 1.20.0). Altogether 779 mRNA were differentially regulated, among which 536 mRNA were upregulated after YTHDF2 KD. This study provides a gene list which shows differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus.
2023-01-19 | GSE171790 | GEO
Project description:To identify the target mRNAs of the m6A reader protein YTHDF1 and YTHDF2, we carired out anti YTHDF1 and anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P6-P8 wild type mouse cerebellum was pulled down by rabbit polyclonal anti-YTHDF1 (proteintech) or polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input and any fold change greater than 2 was considered enriched. Finally, Biological replicates of anti-YTHDF1 RIP-Seq and anti-YTHDF2 RIP-Seq identified 506 and 596 mRNAs transcripts, respectively. This study provides gene lists which shows mRNA binding with YTHDF1 and YTHDF2 in mouse cerebellum.
2021-12-10 | GSE153689 | GEO
Project description:total mRNA profiles of 4-day-old Col (WT), MYB30 knockout mutant (myb30) and MYB30-OE were generated by deep sequencing, in triplicate, Sequencing was carried out with the Illumina HiSeq 2000 platform and the resulting reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10) with TopHat (http://tophat.cbcb.umd.edu). Transcript expression was evaluated by cuffdiff (http://cufflinks.cbcb.umd.edu), and transcript abundance was estimated by fragments per kilobase of exon model per million mapped fragments (FPKM). Differentially expressed genes were selected using Student’s t-test with P<0.05. qRT–PCR validation was performed using SYBR Green assays.
2020-04-14 | GSE141145 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: RNA from 14-day-old seedlings of wild-type and pkl was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings. 14-day-old seedling of WT and pkl were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.
2022-12-12 | GSE186152 | GEO
Project description:Purpose: To study the alteration of whole transcriptome of Lewis lung carcinoma (LLC) cells after the decreasing of malignant properties of tumor by treatment of tumor-bearing mice with RNase A. Methods: Whole transcriptome profile of Lewis lung carcinoma before and after RNase A treatment were generated by deep sequencing using SOLiD 5.5. The sequence reads were mapped by Bioscope 1.3 software, differential expression was evaluated by Cufflinks v.2.0.1 package. Results: Difference in expression was found for 966 genes. Conclusions: Our study represents the first detailed analysis of alteration of transcriptome of Lewis lung carcinoma after the decrease of malignant prtoperties of the tumor (proliferation and invasion) by RNase A. Whole transcriptome profile of Lewis lung carcinoma before and after RNase A treatment were generated by deep sequencing using SOLiD 5.5.
2014-12-03 | E-GEOD-63758 | biostudies-arrayexpress