Ontology highlight
ABSTRACT:
PROVIDER: PRJNA494326 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7948470.fastq.gz | Fastqsanger.gz | |||
| SRR7948480.fastq.gz | Fastqsanger.gz | |||
| SRR7948471.fastq.gz | Fastqsanger.gz | |||
| SRR7948481.fastq.gz | Fastqsanger.gz | |||
| SRR7948462.fastq.gz | Fastqsanger.gz |
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Project description:Genomic Profiling in Cancer Patients (Breast Cancer Paired Tumor Samples)
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Project description:Genomic Profiling in Cancer Patients (Breast Cancer Paired Tumor Samples)
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Project description:To comprehensively characterize microRNA (miRNA) expression in breast cancer, we performed the first extensive next-generation sequencing expression analysis of this disease. We sequenced small RNA from tumors with paired samples of normal and tumor-adjacent breast tissue. Our results indicate that tumor identity is achieved mainly by variation in the expression levels of a common set of miRNAs rather than by tissue-specific expression. We also report 361 new, well-supported miRNA precursors. Nearly two-thirds of these new genes were detected in other human tissues and 49% of the miRNAs were found associated with Ago2 in MCF7 cells. Ten percent of the new miRNAs are located in regions with high-level genomic amplifications in breast cancer. A new miRNA is encoded within the ERBB2/Her2 gene and amplification of this gene leads to overexpression of the new miRNA, indicating that this potent oncogene and important clinical marker may have two different biological functions. In summary, our work substantially expands the number of known miRNAs and highlights the complexity of small RNA expression in breast cancer. Sequencing of approximately 18-35 nt small RNAs from paired samples of normal, tumor and tumor-adjacent tissue for five breast cancer patients
2012-07-06 | E-GEOD-39162 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of tumor adjacent normal tissue from patients with invasive breast cancer, as well as tissue from women undergoing reduction mammoplasty or prophylactic surgery. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in snap frozen breast tissue. Samples included 70 tumor-adjacent normal breast tissue with invasive disease, 8 tissues from breast prophylactic patients, and 18 tissues from breast reduction patients.
2015-04-15 | GSE67919 | GEO
Project description:Future improvements in the field of breast cancer prevention, diagnosis and treatment require deeper knowledge and better understanding of the molecular processes and signaling pathways that lead to the transformation of normal cells to cancer ones and the disease progression. Quantitative proteome profiling of fresh frozen breast tissue and tumor samples may accelerate and facilitate this process. Liquid chromatography (LC) hyphenated to tandem mass spectrometry (MS/MS) technique in data-independent SWATH acquisition mode is a powerful tool for such profiling, because all the precursor ions are fragmented there, which enables label-free identification and quantification of theoretically all proteins in the sample. In this study we performed microLC separation before SWATH-MS analysis. The spectral library, which is necessary for SWATH quantification of the investigated samples, consisted of proteins identified by protein database search of the MS/MS spectra obtained by the information-dependent acquisition (IDA) screening of both normal human breast tissue and breast tumor samples, which were additionally enriched in low abundant proteins by immunoaffinity depletion from 14 high abundant serum proteins. Using the described methodology we detected 547 proteins in all qualitative experiments, which served then as a spectral library for further label-free SWATH quantification of separate breast tumor and corresponding normal breast tissue samples of 8 patients. Among them, 299 proteins were successfully quantified. Levels of 188 of them varied significantly (p<0.05) between normal breast tissue and breast tumor samples. 31proteins were up-regulated and 14 were down-regulated at least two fold in breast tumors comparing to normal breast tissues.
2026-03-16 | PXD008408 | Pride
Project description:Metastasis is responsible for the majority of deaths in a variety of cancer types, including breast cancer. Although several factors or biomarkers have been identified to predict the outcome of patients with breast cancer, few studies have been conducted to identify metastasis-associated biomarkers. Quantitative iTRAQ proteomics analysis was used to detect differentially expressed proteins between lymph node metastases and their paired primary tumor tissues from 23 patients with metastatic breast cancer. Immunohistochemistry was performed to validate the expression of two upregulated (EpCAM, FADD) and two downregulated (NDRG1, αB-crystallin) proteins in 190 paraffin-embedded tissue samples. These four proteins were further analyzed for their correlation with clinicopathological features in 190 breast cancer patients. We identified 637 differentially regulated proteins (397 upregulated and 240 downregulated) in lymph node metastases compared with their paired primary tumor tissues. Furthermore, bioinformatics analysis using GEO profiling confirmed the difference in the expression of EpCAM between metastases and primary tumors tissues. Two upregulated (EpCAM, FADD) and two downregulated (NDRG1, αB-crystallin) proteins were associated with the progression of breast cancer. Obviously, EpCAM plays a role in the metastasis of breast cancer cells to the lymph node. We further identified αB-crystallin as an independent biomarker to predict lymph node metastasis and the outcome of breast cancer patients.
2019-08-29 | PXD013931 | Pride
Project description:We identified total 174 significantly differentially expressed miRNAs between tumors and the normal tissues, and 109 miRNAs between serum from patients and serum from healthy individuals. There are only 10 common miRNAs. This suggests that only a small portion of tumor miRNAs are released into serum selectively. Interestingly, the expression change pattern of 28 miRNAs is opposite between breast cancer tumors and serum. Functional analysis shows that the differentially expressed miRNAs and their target genes form a complex interaction network affecting many biological processes and involving in cancer-related pathways such as prostate, basal cell carcinoma, acute myeloid leukymia, and more. A bunch of miRNAs have been demonstrated to be aberrantly expressed in cancer tumor tissue and serum. The miRNA signatures identified from the serum samples could serve as potential noninvasive diagnostic markers for breast cancer. The roles of the miRNAs in cancerigenesis is unclear. In this study, we generated the expression profiles of miRNAs from the paired breast cancer tumors, normal, tissue, and serum samples from eight patients using small RNA-sequencing. Serum samples from eight healthy individuals were used as normal controls.
2014-04-10 | E-GEOD-56614 | biostudies-arrayexpress
Project description:Because of limited clinical cases, the natural history of occult breast cancer (OBC) is poorly understood and its proteomic signature remains unknown. We performed a quantitative proteomic analysis for tissue samples of metastatic lymph nodes from 3 OBC patients, and paired tissue samples of metastatic lymph nodes and primary tumor from 3 Non-OBC patients.
2025-01-31 | PXD052744 | Pride
Project description:Ductal carcinoma in situ (DCIS) is a precursor lesion that can give rise to invasive breast cancer (IBC). It has been proposed that both the nature of the lesion and the tumor microenvironment play key roles in progression to IBC. Here, laser capture microdissected tissue samples from epithelium and stroma in normal breast, pure DCIS, and pure IBC were employed to define key gene expression profiles associated with disease progression. Tumor and matching stroma were profiled for 9 DCIS patients, 10 IBC patients, and 3 normal breast. Differential gene expression was evaluated for paired normal stroma versus normal epitelium samples, paired DCIS stroma versus DCIS epitelium samples, paired IBC stroma versus IBC epitelium, IBC stroma versus DCIS stroma, and IBC epithelium versus DCIS epithelium.
2012-03-31 | E-GEOD-33692 | biostudies-arrayexpress