Expression profiling of ramie genes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666067 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12727256_1.fastq.gz | Fastqsanger.gz | |||
| SRR12727256_2.fastq.gz | Fastqsanger.gz | |||
| SRR12727257_1.fastq.gz | Fastqsanger.gz | |||
| SRR12727257_2.fastq.gz | Fastqsanger.gz | |||
| SRR12727258_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:To aid the annotation of the genome of cultivated (ZSZ1) and wild (QYZM) ramie and characterize the expression profiling, the root, stem and leaves from these two varieties were performed for transcriptome sequencing. Our results generated 20,693 and 19,498 predicted genes from QYZM and ZSZ1 genome. of them, 17,983 QYZM genes and 17,998 ZSZ1 expressed in at least one of these three examined tissues.
2020-09-29 | GSE158630 | GEO
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
Project description:Ramie fibers extracted from the stem barks have been utilized for thousands years in China, and its biosynthetic mechanism is poorly understood. Here, we have characterized and compared the expression profiling of the barks from the top and middle part of stem where the secondary cellular walls (SCWs) of fiber cell have not initiated growth and was thickening, respectively; resulting in 4,520 differential expression (DE) protein-coding transcripts (PCTs), 1,287 DE long noncoding RNAs (lncRNAs), 88 DE miRNAs and 78 DE circular RNAs (circRNAs). Among the 4,520 DE PCTs, 75 were identified to be the homolog of the Arabidopsis SCW-biosynthetic genes. Overexpression of whole_GLEAN_10014861 (a homolog of SND1) in Arabidopsis caused a significant up-regulation in the expression of AtMYB46 and AtMYB83 that are two key regulators for SCW biosynthesis, thus conferring more fiber cells, along with a remarkable thickening in the SCWs of these cells. Bioinformatic prediction revealed 14 of the 75 homolog targeted by 16 noncoding RNAs (including 8 miRNAs and 8 lncRNAs), and two involved in the competing endogenous RNAs networks, indicating a complex regulatory network for the SCW biosynthesis of bast fiber in ramie. This study provides important insights into the bast fiber biosynthesis of ramie.
2019-05-02 | GSE130587 | GEO
Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability.
2013-04-23 | GSE46253 | GEO
Project description:Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie.
2015-08-21 | GSE60583 | GEO
Project description:Digital gene expression (DGE) analysis was performed to study differentially expressed genes (DEGs) between CK and P. coffeae challenged (CH) roots of ramie. A total of 10.16 and 8.07 million clean reads were detected in the CK and CH libraries, respectively. A total of 137 genes were identified as DEGs, 117 and 20 of them were up- and down- regulated respectively, in response to P. coffeae infection. Roots samples of Pratylenchus coffeae infected(E2) and un-infected (E1) ramie were RNA-Seq sequenced to compare differented expressed genes.
2015-01-20 | E-GEOD-64974 | biostudies-arrayexpress
Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability. 3' tag-based DGE libraries were generated to exam the differentially expressed gene between drought-stressed and well-watered ramie
2013-04-23 | E-GEOD-46253 | biostudies-arrayexpress
Project description:Digital gene expression (DGE) analysis was performed to study differentially expressed genes (DEGs) between CK and P. coffeae challenged (CH) roots of ramie. A total of 10.16 and 8.07 million clean reads were detected in the CK and CH libraries, respectively. A total of 137 genes were identified as DEGs, 117 and 20 of them were up- and down- regulated respectively, in response to P. coffeae infection.
2015-01-20 | GSE64974 | GEO
Project description:Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie. A total of four samples, two replicates of control plants (CO1 and CO2) and two replicates of cadmium-stressed plants (CdS1 and CdS2) were used for RNA-seq.
2015-08-21 | E-GEOD-60583 | biostudies-arrayexpress
Project description:Whole transcriptome profiling of bast fibers of ramie
| PRJNA540688 | ENA