RNA-seq analysis of CaSki/SiHa/HeLa cell lines
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA663801 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12650973_1.fastq.gz | Fastqsanger.gz | |||
| SRR12650973_2.fastq.gz | Fastqsanger.gz | |||
| SRR12650974_1.fastq.gz | Fastqsanger.gz | |||
| SRR12650974_2.fastq.gz | Fastqsanger.gz | |||
| SRR12650975_1.fastq.gz | Fastqsanger.gz |
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Project description:We perfomed RNA-seq analysis using HPV16-postive CaSki and SiHa cells and HPV18-postive HeLa cells for HPV integration and gene expression analyses
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Project description:We present four datasets on proteomics profiling of HeLa and SiHa cell lines associated with the research described in the paper “PROTREC: A probability-based approach for recovering missing proteins based on biological networks”. Proteins in each cell line were acquired by two different data acquisition methods. The first was Data Dependent Acquisition-Parallel Accumulation Serial Fragmentation (DDA-PASEF) and the second was Parallel Accumulation-Serial Fragmentation combined with data-independent acquisition (diaPASEF) . Protein assembly was performed following search against the Swiss-Prot Human database using Peaks Studio for DDA datasets and Spectronaut for DIA datasets . The assembled result contains identified PSMs, peptides and proteins that are above threshold for each HeLa and SiHa sample. Coverage-wise, for DDA-PASEF, approximately 6,090 and 7,298 proteins proteins were quantified for HeLa and SiHA sample, while13,339 and and 8,773 proteins were quantified by diaPASEF for HeLa for SiHa sample respectively.
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Project description:The Galectin-7 gene has been found subregulated in several cervical cancer cell lines and in clinical samples. To study the changes in the cell system after the ectopic expression of Galectin-7, we used microarrays to analyze transcriptome of HeLa and SiHa cancer cell line. Cells were transfected with a viral vector with the Galectin-7 gene and negative controls in 3 biological replicates and analyzed to study gene expression changes. Array data from the same study has also been deposited at ArrayExpress under accession number E-MTAB-3307 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3307/) and E-MTAB-3308 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3308/)
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Project description:Persistent infection by high-risk human papillomaviruses (HPVs) is associated with the development of cervical cancer and a subset of anogenital and head and neck squamous cell carcinomas. Abnormal expression of cellular microRNAs (miRNAs) plays an important role in the development of cancer, including HPV-related tumors. MiRNA expression profile was investigated by microrray analysis in the HPV-positive cervical cancer cell lines SiHa (HPV16-positive cell line derived from a cervical squamous cell carcinoma), CaSki (HPV16-positive cell line derived from a metastatic cervical epidermoid carcinoma), and HeLa (HPV18-positive cell line derived from a cervical adenocarcinoma) and compared with primary HFKs and C33a (HPV-negative cervical cell line).
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Project description:Five human cervical cancer cell lines (HeLa, CaSki, SiHa, C-33A, SW756) and one human normal cervical epithelial cell line HcerEpic were included in the study. Microarray based circRNA expression profiles were acquired using the Arraystar Human circRNA Array (8x15K, Arraystar). We identified circRNAs differentially expressed in human cervical cancer cell lines compared to human normal cervical epithelial HcerEpic cells (control).
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Project description:Galectin-7 transfected HeLa and SiHa cells and controls were implanted in Balb/c mice to generate tumors, we perform microarrays to analyze transcriptome of HeLa and SiHa Galectin-7 positive and controls tumors in 3 biological replicates to study the microenvironment influence in the Galectin-7-related network. Array data from the same study has also been deposited at ArrayExpress under accession number E-MTAB-3306 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3306/) and E-MTAB-3308 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3308/)
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Project description:This study assessed the transcriptional profile of SiHa cells. SiHa is a cervical cancer cell line with integrated HPV16, and was used as a model to study human gene expression in the context of integrated virus. Gene expression in SiHa, calculated by Cufflinks, was scored in windows around the locations of known viral integrations in patients or cell lines to determine if there was an association between gene expression and viral integration. We found that SiHa gene expression was higher near loci of integration for HPV18 vs. HPV16, cervical tissues vs. head and neck cancers, and cervical cancers vs. in vitro integrations. This study provides insight into the factors that may influence where viruses integrate in the human genome.
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Project description:Several copy number altered regions (CNA) have been identified in the genome of cervical cancer, especially amplifications of 3q and 5p. However, the contribution of those alterations to cervical carcinogenesis is still a matter of debate, since genome-wide, there is a lack of correlation between CNAs and gene expression. In this study, we investigated whether the CNAs in cell lines (CaLo, CasKi, HeLa, SiHa), at a gene-by-gene level, are related to changes in gene expression. On average 19.2% of the whole genome of cell lines had CNA. However, only 2.4% consisted of minimal recurrent regions (MRR), common to all cell lines. Whereas 3q had just some sparse common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 11% of genes located in CNAs changed gene expression. In contrast, the rate increased over 3 fold times in MRRs. Chr 5p was confirmed entirely amplified by FISH. In spite of this, at most 32.9% of the explored genes in 5p (n=202) were de-regulated. In 3q, the rate was just 11.8%. Even in 3q26, which had five MRRs and 38.7% of SNPs was gained recurrently, the rate rose slightly to 13.6% (10 out of 73). Interestingly, up to 16% of de-regulated genes in 5p and 80% in 3q26 were down-regulated, suggesting additional factors are involved in gene repression. The de-regulated genes in 3q and 5p were found in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, the rate of down-regulated genes rose steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). This suggests partial gene amplification as a mechanism of silencing gene expression. Additional genes were identified up- or down-regulated in 5p and 3q, which could be involved in cervical carcinogenesis, especially implicated in apoptosis. Those include CLPTM1L, AHRR, PDCD6 and DAP in 5p and TNFSF10 and ECT2 in 3q. Overall, the gene expression and copy number profiles suggest other factors, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments. Further studies are needed to elucidate how these mechanisms regulate gene expression. We analyzed four cervical cancer cell lines and normal exocervix tissue from 10 healthy female subjects using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Biological replicates were performed for the cell lines. biological replicate: Calo-a, Calo-b biological replicate: Caski-a, Caski-b biological replicate: Hela-a, Hela-b biological replicate: Siha-a, Siha-b
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