Ontology highlight
ABSTRACT:
PROVIDER: PRJNA763504 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15904141_1.fastq.gz | Fastqsanger.gz | |||
| SRR15904141_2.fastq.gz | Fastqsanger.gz | |||
| SRR15904142_1.fastq.gz | Fastqsanger.gz | |||
| SRR15904142_2.fastq.gz | Fastqsanger.gz | |||
| SRR15904143_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
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Project description:We used RNA-seq to generate the transcriptional profile of 7 days old WT, smxl5-1, smxl4-1 smxl5-1 and smax1-2 Arabidopsis mutant seedlings. We then used statistical analysis to identify differentially expressed genes that potentially contribute to the smxl5-1, smxl4-1 smxl5-1 and smax1-2 mutant phenotype.
2022-10-01 | GSE71517 | GEO
Project description:To understand the role of SMAX1 and SMXL2 in water stress response, we have carried out comparative expression analysis of the smax1 smxl2 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent's whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.
2022-08-01 | GSE196838 | GEO
Project description:Karrikins (KARs) are a class of butenolide molecules found in the smoke of burned plant material that can induce germination of many plant species that emerge after fire. Intriguingly, KAR perception is widely conserved and not limited to fire-followers. For example, germination of dormant Arabidopsis thaliana seeds can also be stimulated by KARs. Additionally, KAR treatment enhances responses of seedlings to light. These responses include inhibition of hypocotyl elongation, enhancement of cotyledon expansion, and transcriptional upregulation of light-responsive genes not only in Arabidopsis but also in Brassica tournefortii. Although the core KAR signaling mechanism, consisting of KAI2-SCF/MAX2-mediated degradation of SMAX1 and SMXL2, is well described, it remains elusive how SMXL degradation leads to downstream growth responses. In this study, we analyse the role of BBX20 in the KAR signaling pathway through both chemical and genetic approaches using knock-out mutants. We find that BBX20, together with its close homologue BBX21, is essential for KAR-induced inhibition of hypocotyl elongation and anthocyanin accumulation. Our detailed genetic analysis suggests that BBX20 and BBX21 act in a HY5-dependent transcriptional module downstream of SMAX1 and SMXL2. While RNA-seq analysis revealed large-scale transcriptional changes in the smax1 smxl2 mutant, our results clearly suggest that BBX20 and BBX21 are required for a subset of SMAX1/SMXL2-dependent transcriptional regulation. Overall, our data suggest that the KAR signaling pathway promotes the activity of the HY5-BBX transcriptional module and that this module represents a point of convergence between KAR and light signaling.
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Project description:To explore the possible role of Nsd2 in kidney cancer, the gene expression profile of kisney tissues from KMN (Ksp-Cre; Myc OE/+; Nsd2 OE/+) and littermate KM (Ksp-Cre; Myc OE/+) mice was examined by RNA sequencing(RNA-Seq).
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Project description:Karrikins (KARs) are a class of butenolide molecules found in smoke. KARs regulate many aspects of plant development and environmental responses, including Seed germination, hypocotyl elongation, leaf shape, root development, and resistance to drought, salt, and heat stress. The transcriptional repressor proteins SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-like2 (SMXL2) integrate karrikin signaling by repressing gene expression through direct binding to promoters or through inhibiting activities of transcription factors. To elucidate the mechanism by which SMAX1 and SMXL2 mediate KAR signaling, we performed immunoprecipitation followed by mass spectrometry (IP-MS) analysis and identified peptides in transgenic seedlings that overexpress GFP, SMAX1-GFP, and SMXL2-GFP, respectively.
2024-06-22 | PXD052400 | Pride
Project description:We report RNA sequencing (RNA-seq) data WT, atf-4 loss-of-function mutants, and ATF-4 OE worms under non-stressed conditions. Three independent biological replicates were prepared for each sample, and worms were harvested at L4 stage.
2021-05-05 | GSE173799 | GEO
Project description:Intervention type:DRUG
Name of intervention:Huaier
Dose form / Japanese Medical Device Nomenclature:GRANULES
Route of administration / Site of application:ORAL
Dose per administration:20?
g
Dosing frequency / Frequency of use:OTHER, SPECIFY
20g? per day
Planned duration of intervention:3 months to extending if necessary
Intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary
detailes of teratment arms:hepatocellular carcinoma, breast cancer, colorectal cancer and related gastrointestinal cancers, urologic cancers including prostate cancer, pancreas cancer, and lung cancer, etc.
Comparative intervention name:None
Dose form / Japanese Medical Device Nomenclature:
Route of administration / Site of application:
Dose per administration:
Dosing frequency / Frequency of use:
Planned duration of intervention:
Intended dose regimen:
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.
Study Design: Comparative test, None, No, open(masking not used), EXPLORATORY
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Project description:Purpose: To assess global changes in gene expression in response to FGM4 Methods: mycelium mRNA profiles of 3-day-old wild-type PH-1,∆fgm4,WT-OE::FGM4 and ∆fg3_54-OE::FGM4 were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500. Results: We mapped more than 31 million clean sequence reads per sample to the Fusarium graminearum PH-1 genome. RNA-seq data confirmed that expression of all FG3_54 cluster member genes was elevated in WT-OE::FGM4 compared to the remaining strains, while expression of neighboring genes outside the cluster remained unchanged. Conclusions: Our study represents that FGM4 functions as a cluster-specific transcriptional regulator.
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Project description:The scope of the project is to find DNA binding sites of the DNA binding protein AtDEK3. For the experiments AtDEK3 overexpressor (OE) plants have been obtained. The AtDEK3 was tagged with a CFP-tag. With ChIP the protein was pulled down and eluted DNA was send for sequencing. Gene ontology (GO) term classification of genes enriched for AtDEK3 binding indicated that AtDEK3 target genes are involved in diverse biological processes. ChIP Seq of three indenpendendt AtDEK3 OE and their respective inputs were used.
2014-11-14 | E-GEOD-55893 | biostudies-arrayexpress