Genome-wide profiling of non-small cell lung cancer derived cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA557651 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9866460_1.fastq.gz | Fastqsanger.gz | |||
| SRR9866460_2.fastq.gz | Fastqsanger.gz | |||
| SRR9866470_1.fastq.gz | Fastqsanger.gz | |||
| SRR9866470_2.fastq.gz | Fastqsanger.gz | |||
| SRR9866461_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 40 |
Similar Datasets
Project description:We established patient-derived cancer cell (PDC) cultures from metastatic non-small cell lung cancer, including two pairs of matched EGFR-mutant PDCs pre-treatment and after resistance to tyrosine-kinase inhibitors (TKIs), and then performed whole-exome and RNA sequencing to delineate their genomic architecture. For validation, we analyzed independent cohorts of primary NSCLC.
2019-12-31 | GSE135164 | GEO
Project description:GENOME-WIDE CpG ISLAND METHYLATION ANALYSIS IN NON-SMALL CELL LUNG CANCER PATIENTS
| PRJNA147769 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE29248: Genome-wide analysis of microRNA expression in Non-small Cell Lung Cancer GSE29249: Genome-wide analysis of gene expression in Non-small Cell Lung Cancer Refer to individual Series
2012-09-16 | E-GEOD-29250 | biostudies-arrayexpress
Project description:Purpose: Generate genome-wide methylation profiles of non-small cell lung carcinomas (NSCLC) and their matching lung tissues for detection of hypermethylated and hypomethylated regions present in the tumors. Methods: MethylCapture followed by next-generation sequencing (Illumina GAIIx) of 7 nsclc tumor samples and paired lung tissues in replicated, plus one cell line, 2 fully artificially methylated and 2 fully artificially unmethylated controls. Normalization of methylation reads based on CpG coupling factor–method. Relative methylation scores (rms) in 500bp non-overlapping windows. 90th percentile of rpm (reads per million) values for all 500bp genome-wide windows, with rpm <1.33 were considered. Distributions of 10bp bins rms values within each 500bp genomic region were compared using both one-sided Student’s t-test and one-sided Wilcoxon rank-sum test. Testing was done separately for hypo- and hypermethylation and p-value threshold of 10-18. Results: MethylCap-seq data revealed strong positive correlation between replicate experiments and between paired tumor/lung samples. 14472 differentially methylated regions (DMR) with non-overlapping 500 bp windows were found. 57 DMRs were present in all NSCLC tumors. 287 were unique for squamous-cell carcinomas and 26 unique for adenocarcinomas. While hypomethylated DMRs did not correlate to any particular functional category of genes, the hypermethylated DMRs were strongly associated with genes encoding transcriptional regulators. Furthermore, subtelomeric regions and satellite repeats were hypomethylated in the NSCLC samples. Conclusion: We provide a resource containing genome-wide DNA methylation maps of NSCLC and their paired lung tissues, and comprehensive lists of known and novel DMRs and associated genes in NSCLC. The DMRs can be in further studies to develop sensitive biological markers for NSCLC, which may enable non-invasive diagnosis and early detection of the disease, and potentially allow histological classification. MethylCap-seq of 7 nsclc tumor samples and paired lung tissues, plus 2 fully methylated and 2 fully unmethylated controls.
2012-10-05 | E-GEOD-41343 | biostudies-arrayexpress
Project description:Non-small Cell Lung Cancer Brain Metastasis Atlas
| PRJNA926591 | ENA
Project description:RNA profilling of non-small cell lung cancer
| PRJEB27606 | ENA
Project description:We present data of global proteomes for non-small cell lung cancer for squamous cell and adenocarcinoma, and for normal adjacent tissue.
2024-12-17 | PXD054390 | Pride
Project description:This series contain 36 samples obtained from human lung tissue and includes the following: 7 Adenocarcinoma samples. 16 Squamous cell carcinoma samples. 1 AdenoSquamous sample. 2 Renal Metastasis. 1 Colon metastasis. 7 normal lung tissue adjacent to the tumors. 2 commercial normal lung RNA. Keywords = Lung Keywords = Non Small Cell Lung Cancer Keywords = Adenocarcinoma Keywords = Squamous Cell Carcinoma Keywords = Normal Lung. Keywords: other
2005-07-20 | GSE1987 | GEO
Project description:Exosomes play important roles in intercellular communication through the delivery of their cargoes, which include proteins, lipids, and RNAs. Increasingly, multiple studies have reported the association between exosomal small non-coding RNAs and cancer, due to their regulatory functions in gene expression. Hence, analysis of the features of small non-coding RNA expression and their incorporation into exosomes is important for cancer research. Here, we performed deep sequencing to investigate the expression of small RNAs in plasma exosomes from lung adenocarcinoma patients, lung squamous cell carcinoma patients, and healthy controls. We found that 5’ YRNA hY4-derived fragments are significantly upregulated in non-small cell lung cancer (NSCLC) exosomes, and may serve as a novel class of circulating biomarkers for NSCLC diagnosis. We also identified that the RNY4P7 gene on chromosome 2 may not be a pseudogene, because the corresponding transcript hY4 reverse fragment was detected in exosomes and cells. Further, we demonstrated that a panel of small RNAs, including miR-451a and miR-122-5p, may be selectively sorted into NSCLC exosomes. Overall, our studies have indicated a wider range of biological effects in NSCLC that may be mediated by exosomal small RNAs than previously known.
2018-02-14 | GSE103149 | GEO
Project description:Purpose: Generate genome-wide methylation profiles of non-small cell lung carcinomas (NSCLC) and their matching lung tissues for detection of hypermethylated and hypomethylated regions present in the tumors. Methods: MethylCapture followed by next-generation sequencing (Illumina GAIIx) of 7 nsclc tumor samples and paired lung tissues in replicated, plus one cell line, 2 fully artificially methylated and 2 fully artificially unmethylated controls. Normalization of methylation reads based on CpG coupling factor–method. Relative methylation scores (rms) in 500bp non-overlapping windows. 90th percentile of rpm (reads per million) values for all 500bp genome-wide windows, with rpm <1.33 were considered. Distributions of 10bp bins rms values within each 500bp genomic region were compared using both one-sided Student’s t-test and one-sided Wilcoxon rank-sum test. Testing was done separately for hypo- and hypermethylation and p-value threshold of 10-18. Results: MethylCap-seq data revealed strong positive correlation between replicate experiments and between paired tumor/lung samples. 14472 differentially methylated regions (DMR) with non-overlapping 500 bp windows were found. 57 DMRs were present in all NSCLC tumors. 287 were unique for squamous-cell carcinomas and 26 unique for adenocarcinomas. While hypomethylated DMRs did not correlate to any particular functional category of genes, the hypermethylated DMRs were strongly associated with genes encoding transcriptional regulators. Furthermore, subtelomeric regions and satellite repeats were hypomethylated in the NSCLC samples. Conclusion: We provide a resource containing genome-wide DNA methylation maps of NSCLC and their paired lung tissues, and comprehensive lists of known and novel DMRs and associated genes in NSCLC. The DMRs can be in further studies to develop sensitive biological markers for NSCLC, which may enable non-invasive diagnosis and early detection of the disease, and potentially allow histological classification.
2012-10-05 | GSE41343 | GEO