Small RNA-Sequencing of PDAC tissues and control samples.
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR852089.fastq.gz | Fastqsanger.gz | |||
| ERR852090.fastq.gz | Fastqsanger.gz | |||
| ERR852091.fastq.gz | Fastqsanger.gz | |||
| ERR852092.fastq.gz | Fastqsanger.gz | |||
| ERR852093.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 11 |
Similar Datasets
Project description:FASTQ Sequencing files of 5 healthy pancreas tissues and 6 pancreatic ductal adenocarcinoma (PDAC) tissues. Analysis of data is presented in the manuscript: Next generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer in BMC Molecular Cancer.
2015-05-15 | E-MTAB-3494 | biostudies-arrayexpress
Project description:Background/Aims: Microarray-based comparative genomic hybridisation (CGH) has allowed high-resolution analysis of DNA copy number alterations across the entire cancer genome. Recent advances in bioinformatics tools enable us to perform a robust and highly sensitive analysis of array CGH data and facilitate the discovery of novel cancer-related genes. Methods: We analysed a total of 29 pancreatic ductal adenocarcinoma (PDAC) samples (six cell lines and 23 microdissected tissue specimens) using 1 Mb-spaced CGH arrays. The transcript levels of all genes within the identified regions of genetic alterations were then screened using our Pancreatic Expression Database. Results: In addition to 238 high-level amplifications and 35 homozygous deletions, we identified 315 minimal common regions of “non-random” genetic alterations (115 gains and 200 losses) which were consistently observed across our tumour samples. The small size of these aberrations (median size of 880 kb) contributed to the reduced number of candidate genes included (on average 12 Ensembl-annotated genes). The database has further specified the genes whose expression levels are consistent with their copy number status. Such genes were UQCRB, SQLE, DDEF1, SLA, ERICH1 and DLC1, indicating that these may be potential target candidates within regions of aberrations. Conclusion: This study has revealed multiple novel regions that may indicate the locations of oncogenes or tumour suppressor genes in PDAC. Using the database, we provide a list of novel target genes whose altered DNA copy numbers could lead to significant changes in transcript levels in PDAC. (Harada et al. Pancreatology) Keywords: pancreatic ductal adenocarcinima, tissue microdissection, array CGH, genetic alterations A panel of 23 microdissected PDAC tissues and 6 PDAC-derived cell lines were analysed using Sanger's CGH arrays with 1 Mb resolution. Clinical info of the samples used is provided as a supplementary file.
2008-12-16 | E-GEOD-9672 | biostudies-arrayexpress
Project description:To determine the lncRNA and mRNA expression profile in PDAC and matched non-tumor tissues, we uesed lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs and mRNAs in PDAC and matched non-tumor tissues.
2017-07-11 | GSE101094 | GEO
Project description:Pancreatic adenocarcinoma (PDAC) is one of the most lethal human malignancies and a major health problem. Patient-derived tumor xenografts (PDTXs) have been increasingly used as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. Extensive multiomics characterization of these PDTXs have demonstrated their utility as a suitable model for preclinical studies, representing the diversity of the primary cancers. We performed a multi-factorial integrative analysis of genome-wide ChIP-seq on multiple histone modifications, as well as RNA-seq on subcutaneous PDTXs from 24 PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). In the dataset, ChIP-seq for five distinct histone marks (H3K4me1, H3K27ac, H3K4me3, H3K27me3, and H3K9me3) and RNA-seq was carried out to generate new knowledge on the epigenetic landscapes underlying the heterogeneity of PDAC tissues grown in this manner.
2018-05-29 | E-MTAB-5632 | biostudies-arrayexpress
Project description:RNA sequencing of pancreatic adenocarcinoma (PDAC) xenograft samples
| PRJEB19942 | ENA
Project description:Pancreatic adenocarcinoma (PDAC) is one of the most lethal human malignancies and a major health problem. Patient-derived tumor xenografts (PDTXs) have been increasingly used as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. Extensive multiomics characterization of these PDTXs have demonstrated their utility as a suitable model for preclinical studies, representing the diversity of the primary cancers. We performed a multi-factorial integrative analysis of genome-wide ChIP-seq on multiple histone modifications, as well as RNA-seq on subcutaneous PDTXs from 24 PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). In the dataset, ChIP-seq for five distinct histone marks (H3K4me1, H3K27ac, H3K4me3, H3K27me3, and H3K9me3) and RNA-seq was carried out to generate new knowledge on the epigenetic landscapes underlying the heterogeneity of PDAC tissues grown in this manner. <br>Note: Sample phenotypes have been updated on 2020-09-11 to correct the swapped labels between \"classical\" and \"basal\" phenotypes.
2018-05-29 | E-MTAB-5639 | biostudies-arrayexpress
Project description:Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina).
2014-07-08 | GSE49149 | GEO
Project description:Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina). 167 pancreatic tumors (PDAC) x 29 adjacent -non tumor samples.
2014-07-08 | E-GEOD-49149 | biostudies-arrayexpress
Project description:Background/Aims: Microarray-based comparative genomic hybridisation (CGH) has allowed high-resolution analysis of DNA copy number alterations across the entire cancer genome. Recent advances in bioinformatics tools enable us to perform a robust and highly sensitive analysis of array CGH data and facilitate the discovery of novel cancer-related genes. Methods: We analysed a total of 29 pancreatic ductal adenocarcinoma (PDAC) samples (six cell lines and 23 microdissected tissue specimens) using 1 Mb-spaced CGH arrays. The transcript levels of all genes within the identified regions of genetic alterations were then screened using our Pancreatic Expression Database. Results: In addition to 238 high-level amplifications and 35 homozygous deletions, we identified 315 minimal common regions of “non-random” genetic alterations (115 gains and 200 losses) which were consistently observed across our tumour samples. The small size of these aberrations (median size of 880 kb) contributed to the reduced number of candidate genes included (on average 12 Ensembl-annotated genes). The database has further specified the genes whose expression levels are consistent with their copy number status. Such genes were UQCRB, SQLE, DDEF1, SLA, ERICH1 and DLC1, indicating that these may be potential target candidates within regions of aberrations. Conclusion: This study has revealed multiple novel regions that may indicate the locations of oncogenes or tumour suppressor genes in PDAC. Using the database, we provide a list of novel target genes whose altered DNA copy numbers could lead to significant changes in transcript levels in PDAC. (Harada et al. Pancreatology) Keywords: pancreatic ductal adenocarcinima, tissue microdissection, array CGH, genetic alterations
2008-12-17 | GSE9672 | GEO
Project description:Expression profiling of 8 normal pancreatic and 14 PDAC tissues. Data was generated from Affymetrix arrays. Results provide a global profile of over 50,000 genes in normal and tumorous tissues, and comparison of the differentially expressed genes between the normal and tumor groups. Gene expression was profiled and compared between normal pancreatic and PDAC RNA samples globally, using Affymetrix GeneChip® Human Genome U133 Plus 2.0array.
2015-08-13 | E-GEOD-71989 | biostudies-arrayexpress