Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1163343 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30736171_1.fastq.gz | Fastqsanger.gz | |||
| SRR30736171_2.fastq.gz | Fastqsanger.gz | |||
| SRR30736172_1.fastq.gz | Fastqsanger.gz | |||
| SRR30736172_2.fastq.gz | Fastqsanger.gz | |||
| SRR30736173_1.fastq.gz | Fastqsanger.gz |
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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..
| 2612481 | ecrin-mdr-crc
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
| 98681 | ecrin-mdr-crc
Project description:To investigate the effect of Burkholderia fungorum (BF) on cholangiocarcinoma cells, we treated the cell lines with bacterial supernatant and performed transcriptome sequencing. By transcriptome sequencing, we quantified the differentially expressed genes in control and experimental groups. The results of GO and KEGG functional enrichment analysis showed that the differentially expressed genes were mainly involved in some biological processes of metabolism and amino acid synthesis. We inferred that the transcriptome characterization can help us understand the relationship between bacterium and tumor cell metabolism.
2022-12-31 | GSE182319 | GEO
Project description:In order elucidate the key signaling pathways in choroidal neovascularization, we induced choroidal angiogenesis by laser photocoagulation in 12 tree shrews and obtained mRNA profiles of their choroids and retinas by high-throughput transcriptome sequencing. Gene ontology(GO) and kyoto encyclopedia of genes and genomes(KEGG) enrichment analysis, hierarchical cluster analysis, weighted gene co-expression network analysis, protein-protein interaction (PPI) network analysis, and reverse transcription quantitative PCR (RT-qPCR) were performed.
2021-03-21 | E-MTAB-10198 | biostudies-arrayexpress
Project description:shRNA was used to knock down SLC2A10 VSMCs. The effectiveness of gene interference was tested by qPCR. Transcriptome sequencing was performed and FASTQ files from RNA- seq experiments were clipped and trimmed. KEGG enrichment analysis on differently expressed genes was performed.
2024-11-24 | GSE190244 | GEO
Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .
2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress
Project description:Objective: To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology. Methods: Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis. Results: Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes. Conclusion: The whole transcript of CPAM shows obvious gene up- and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.
2022-12-07 | GSE190620 | GEO
Project description:The purpose of this study was to clarify the possible mechanism of common carp brain injury after exposure to lead through transcriptome analysis. Transcriptome analysis showed that 2141 differentially expressed genes were identified. Among these, 502 genes were up-regulated and 1639 genes were down-regulated. Meanwhile, GO enrichment analysis showed Transport, biological_process, DNA-templated (regulation of transcription) and signal transduction contained the most differential genes in the biological process. Furthermore, KEGG pathway enrichment analysis showed Ion channels, GnRH signaling pathway, cell adhesion molecules, Wnt signaling pathway, and calcium signaling pathway were significantly enriched. In addition, 10 differentially expressed genes were selected for qRT-PCR detection, and the results demonstrated that the selected genes exhibited the same trends with the RNA-Seq results, which indicates the transcriptome sequencing data is reliable. In conclusion, the above results provide a theoretical basis for clarifying the relationship between lead exposure and brain injury in common carp and for further studying of the genes related to lead poisoning.
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Project description:The study involved the proteomic sequencing of extracellular vesicles secreted by Giardia duodenalis, statistical analysis of detected proteins, and GO analysis and enrichment KEGG analysis of proteins
2025-05-07 | PXD054439 | Pride
Project description:The goal of this study is to investigate the effect of ABCB6 inhibition on the transcriptome level of melanoma cell line MNT-1. We performed next-generation sequencing (NGS) on both ABCB6 depleted MNT-1 cells (shABCB6) and unknocked control cells (CTRL). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2500 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the key role of ABCB6 in modulating melanocyte development.
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