Project description:5 colorectal cancer (CRC) tissues and 5 paired non-tumor tissues from CRC patients were indirectly compared using a 17K cDNA microarray.
Project description:DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed. Bisulphite converted DNA from 92 colorectal tumor samples and paired adjacent normal mucosa were hybridised to the Illumina GoldenGate Methylation Cancer Panel I. Additionally, replicates were hybridised for five tumor tissue and their corresponding normal mucosa for reproducibility purposes, totalling 194 samples. Three samples (SAMPLEs 49, 51, and 162) and 50 loci did not reach the quality criteria required regarding the signal-to-noise ratio and were therefore excluded from further analysis. One additional non-tumoral sample (SAMPLE 15) was removed because it exhibited a methylation pattern quiet different from that shown by the rest of normal specimens, which could be indicative of hybridization errors. These Samples and loci are included in the raw data matrix to allow other investigators to use them if different criteria are applied. They have been also included in the Sample tables with missing values in order to preserve the structure of the data across records/files (See 'data processing' section for more details).
Project description:The RNA from two paired normal and colorectal tumor tissue were sequenced by Illumina genome analyzer. 0.8 to 1.1 million reads were generated. Sequencing data was aligned with human RNA, human mitochondrial DNA and human genomic DNA by BWA. Base calling and Phred-like score was calculated by SAMTools. Whole transcriptome sequence of paired normal and tumor tissues obtained from two colorectal cancer patients
Project description:miRNA expression profiles were evaluated in a series of 64 prostate clinical specimens, including 32 cancer and 32 non-neoplastic tissues. For 26 individuals, paired cancer and non-neplastic tissue was available. Tumor and non-neoplastic tissues were obtained, with appropriate informed consent and Institutional Review Board approval, from untreated prostate cancer patients subjected to radical prostatectomy. Freshly frozen surgical blocks were carefully dissected by the pathologist using H&E-stained sections as a template to identify areas containing at least 70% of tumor or normal cells. The total series comprises 64 clinical specimens, of which 32 from cancer areas and 32 from benign areas. For 26 patients, matched tumor and normal samples were available.
Project description:Nine specimens from three colorectal cancer (CRC) patients including adjacent normal tissue, primary tumor, and lever metastasis tissue, and three specimens from 3 CRC patients without liver metastasis were collected for RNA sequencing analysis.
Project description:1,322 morphologically unidentified fragmentary bone specimens were analyzed using MALDI-TOF and a subset of 341 bone specimens with LC-MS/MS in order to characterize their proteome for species identification and potential hominin specimens related to the LRJ transitional period derived from the site Ilsenhöhle Ranis, Germany (50°39.7563’N, 11°33.9139’E).
Project description:Samples were taken from colorectal cancers in surgically resected specimens in 33 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for CIN phynotype Specimens from 33 consecutive stage II and stage III patients who had undergone surgical resection of CRC were studied. Patients with familial adenomatous polyposis and HNPCC were excluded from the study. Specimens from tumors and corresponding normal tissues in surgically resected specimens were snap-frozen in liquid nitrogen and stored at -80degreesC until use. Parallel tumor specimens were formalin fixed and paraffin embedded for histological examination. DNA and RNA was extracted from paired tumor and normal tissue using frozen samples. The patients provided written, informed consent to the collection of specimens, and the local Ethics Committee approved the study protocol. MSI and LOH phenotype analysis were done as follows; Using DNA, we performed the polymerase chain reaction (PCR) and determined the MSI status. In addition to five microsatellite markers recommended by the National Cancer Institute workshop, we also used TP53, D18S46, D18S363 and D18S474.9 We determined LOH status in non–MSI-high tumors, because LOH is rare in MSI-high tumors and also interpretation of LOH is difficult in MSI-high tumors. We defined LOH at each locus as a 50% reduction in the height of one of two allele peaks in tumor DNA relative to non-neoplastic control DNA. LOH was defined as present if any of the markers on the same chromosome show LOH. In order to evaluate the severity of chromosomal instability based on the actual frequency of LOH among evaluable loci, we defined the LOH Ratio (%) as: LOH Ratio (%) = Total number of chromosomes with LOH / Total number of chromosomes that could be evaluated for LOH × 100. Depending on the LOH Ratio, we classified tumors as having high levels of chromosomal instability (CIN-high) (33% < LOH Ratio < 100%) or low levels of chromosomal instability (CIN-low) (0% < LOH Ratio <33%). Furthermore, CIN-high tumors were divided into two subgroups; CIN-high (mild type) (33% < LOH Ratio < 75%) and CIN-high (severe type) (75% < LOH Ratio <100%).