Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Using RNA sequencing to identify key microRNAs and hub genes in the progression of hepatocellular carcinoma

ABSTRACT: This project completed the transcriptome analysis of 6 samples and obtained 12142010 reads Clean Data (after quality control sequencing data). The average clean data volume of each sample was 1833443535 bp , the Q30 base percentage was over 80%, and the GC content was 68.15. % To 46.53%. In this study, we used RNA sequencing and integrated bioinformatics approach to explore hub miRNA-mRNA interactions that are highly associated with hepatocellular carcinoma development. Our data indicated that miR-139-5p is closely related to the overall survival rate of hepatocellular carcinoma patients and directly combines with ITGB8 to regulate its expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE185913 | GEO | 2021/10/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

High-throughput sequencing approach for the identification of lncRNA biomarkers in hepatocellular carcinoma and reveal the effect of ZFAS1 on hepatocellular carcinoma progression（lncRNA and mRNA）

Project description:The aim of this study was to screen abnormal lncRNAs in the progression of hepatocellular carcinoma through high-throughput sequencing, and to screen the biomarkers for prognosis and diagnosis of hepatocellular carcinoma. Transcriptome analysis of 6 samples was completed in this project. A total of 93.581 Gb Clean Data (sequencing Data after quality control) was obtained. The average amount of Clean Data of each sample was 15.597 Gb. The Q30 base percentage was above 93.69 % and GC content was between 44.95% and 50.05%. In conclusion, sequencing analysis provided a landscape for abnormal regulation of lncRNAs, and screened out a significantly different lncRNAs ZFAS1. ZFAS1were found to be overexpressed in hepatocellular carcinoma tissues and correlated with malignant status and prognosis of hepatocellular carcinoma patients, and ZFAS1 silencing inhibited proliferation, migration and invasion of SK-Hep1 cells. The overexpression of miR-582-3p can eliminate the inhibitory effect of ZFAS1 silencing on SK-Hep1 cells, which may be valuable for the diagnosis and treatment of hepatocellular carcinoma. ZFAS1 may be a new potential biomarker for liver cancer. Further studies on the regulatory process of ZFAS1/miR-582-3p will help us to understand the mechanism of the occurrence and development of liver cancer

2021-10-16 | GSE185799 | GEO

MIR100HG regulates CALD1 gene expression by targeting miR-142-5p to affect the progress of bladder cancer cells in vitro revealed by long noncoding RNA sequencing (lncRNA and mRNA)

Project description:This project completed the transcriptome analysis of 6 samples and obtained 79.158 Gb Clean Data (after quality control sequencing data). The average clean data volume of each sample was 13.193 Gb, the Q30 base percentage was over 93.02%, and the GC content was 39.35. % To 46.16%. through lncRNA sequencing, bioinformatics analysis and cell function studies, we found that MIR100HG is a new bladder cancer promoter that regulates the expression of CALD1 gene by targeting miR-142-5p and promotes the proliferation, migration and invasion of bladder cancer cells. These findings provide a new perspective for the study of the pathogenesis and development of bladder cancer, and have the potential as a new target for the diagnosis, prognosis and targeted therapy of bladder cancer.

2021-10-18 | GSE185901 | GEO

HCC prediction after clearance of HCV in chronic hepatitis C II

Project description:We attempted to development prediction methods for hepatocellular carcinoma (HCC) in chronic hepatitis C patients who have been successfully treated by anti-viral therapy. 2565 miRNAs in 139 exosome specimens were analyzed.

2020-01-24 | GSE119159 | GEO

Using lncRNA sequencing to reveal a putative lncRNA-mRNA correlation network and potential role of PCBP1-AS1 in pathogenesis of cervical cancer

Project description:The aim of this study was to construct a lncRNA-mRNA co-expression function network and analyze lncRNAs that might contribute to the pathogenesis of cervical cancer. Transcriptome analysis of 3 cervical cancer samples and 3 adjacent tissue samples was completed in this project.LncRNA-mRNA correlation analysis, enrichment of functions, qPCR, K-M survival, clinicopathology analysis, GSEA and immune infiltration analysis were implemented. Total of 67.600 GB of Clean Data (sequencing Data after quality control) was obtained. The average amount of Clean Data of each sample was 11.267 GB, the percentage of Q30 base was above 91.18%, and the GC content was between 45.46% and 47.18%.Reference species: human;Reference genomic version: GRCH38;Reference genome source: http://asia.ensembl.org/Homo_sapiens/Info/Index;The sequencing data of each sample after quality control was compared with the specified reference genome, and the matching rates ranged from 95.957% to 97.270%, and the unique matching rates ranged from 91.363% to 94.258%. Transcriptomic and lncRNA-mRNA correlation analysis revealed PCBP1-AS1 plays a key role as an independent prognostic factor in patients with cervical cancer.

2021-02-24 | GSE167362 | GEO

Transcriptomes of Wild Type tomato and slstop1 under -Al/+Al treatment

Project description:Purpose: Find SlSTOP1 regulated genes Methods: Total RNA was extracted from 20 days old wild-type tomato and slstop1 mutant plants treated with 0 and 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced. Results:A total of 83.7 GB clean data was obtained by transcriptome sequencing. The clean data of each sample was more than 6.30 GB, and the percentage of q30 base was more than 93.82%. Conclusions: By RNA-seq analysis, we find potential SlSTOP1-regulated genes

2023-08-07 | GSE168433 | GEO

Transcriptomes of Wild Type tomato and slszp1 under +Al treatment

Project description:Purpose: Find SlSZP1 regulated genes Methods: Total RNA was extracted from 20 days old wild-type tomato and slszp1 mutant plants treated with 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced. Results:A total of 40 GB clean data was obtained by transcriptome sequencing. The clean data of each sample was more than 6.11 GB, and the percentage of q30 base was more than 90.98%. Conclusions: By RNA-seq analysis, we find potential SlSZP1-regulated genes

2025-04-20 | GSE201111 | GEO

iTRAQ proteomics of non fibrotic carcinoma on Human Liver

Project description:We present a study of hepatocellular carcinoma developed on non-fibrotic liver (nfHCC) that combines complementary quantitative iTRAQ-based proteomics and phosphoproteomics approaches. Using both approaches, we analyzed a set of 24 samples (18 nfHCC vs 6 non-tumor liver tissue).

2014-09-18 | PXD001253 | Pride

HCC cancer

Project description:Hepatocellular Carcinoma RNA data

| PRJNA337887 | ENA

Transcriptome sequencing was performed on Gossypium barbadense fibers at different developmental stages

Project description:The purpose of this study was to find candidate genes related to fiber strength by comparing the differences in gene expression levels of different samples at different stages of fiber development. Methods: PimaS-7 and 5917, two Gossypium barbadense materials with significant difference in fiber strength, were used as experimental materials. Transcriptome sequencing was performed on the fibers at 0,5,10,15,20,25,30,35 dPA after flowering, with three biological replicates。Sequence reads that were quality-screened were analyzed at the transcriptional subtype level using two methods :Burrows-Wheeler Aligner (BWA), then Aova (Aova) and Tophat, then Cufflinks. Results: Transcriptome analysis of 48 samples was completed, and a total of 317.57Gb of Clean Data was obtained. The Clean Data of all samples reached 5.78Gb, and the percentage of Q30 bases was 92.78% or above.The Clean Reads of each sample were sequenced with the designated reference genome, and the alignment efficiency ranged from 85.56% to 94.79%.Based on the comparison results, alternative splicing prediction analysis, gene structure optimization analysis and discovery of new genes were performed. 7,726 new genes were discovered, of which 6,612 were functional annotations. Conclusion: In this study, RNA-seq technology was used to analyze the changes of gene expression during the development of Gossypium barbadense fiber.Our results suggest that NGS provides a comprehensive and more accurate quantitative and qualitative assessment of RNA content in tissues.we conclusion that based on RNA-seq technology, the genes related to target traits can be obtained quickly.

2022-06-28 | GSE178945 | GEO

Homo sapiens

Project description:Expression data of Hepatocellular Carcinoma

| PRJNA98697 | ENA