Ontology highlight
ABSTRACT:
PROVIDER: PRJNA761768 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15823800_1.fastq.gz | Fastqsanger.gz | |||
| SRR15823800_2.fastq.gz | Fastqsanger.gz | |||
| SRR15823900_1.fastq.gz | Fastqsanger.gz | |||
| SRR15823900_2.fastq.gz | Fastqsanger.gz | |||
| SRR15824000_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 420 |
Similar Datasets
Project description:Formalin-fixed, paraffin-embedded samples from 27 FIT interval CRC and 54 screen-detected CRCs collected in a pilot-program of FIT-based CRC screening in the southwest and northwest regions in the Netherlands, were used in this study. DNA was extracted for 1) Shallow Sequencing (copy number analysis) and 2) TSACP Amplicon Cancer Gene Panel (mutations) of 22 FIT Interval CRCs and 45 screen-detected CRCs.
| EGAD00001006409 | EGA
Project description:Colorectal cancer (CRC) poses one of the most serious threat against human health worldwide, and abnormally expressed c-Myc and p53 are deemed the pivotal driving forces of CRC progression. Here we discovered a lncRNA FIT, which was down-regulated in CRC clinical samples, was transcriptionally suppressed by c-Myc and promoted CRC cells apoptosis by inducing FAS expression. FAS is a p53 target gene, and we found that FIT formed a trimer with RBBP7 and p53 which facilitated p53 acetylation and transcription. Moreover, FIT was capable of retarding CRC growth in mice xenograft model and positively relevant to FAS expression clinically. Thereby our study elucidated the role of lncRNA FIT in human colorectal cancer growth and provides a potential target for anti-CRC drugs.
2022-08-29 | GSE211804 | GEO
Project description:Using genome-scale CRISPR-Cas9 screening, our study revealed KMT2A as a critical regulator of β-catenin-driven CRC progression. To determine the role of KMT2A in β-catenin-mediated transcription, control and KMT2A-ablated DLD1 and SW480 colorectal cancer (CRC) cells were subjected to CHIP-seq analysis using anti-β-catenin and anti-H3K4me3 antibodies. Data obtained from the CHIP-seq experiments indicated a key role of KMT2A in β-catenin binding on active promoters.
2021-05-26 | GSE156081 | GEO
Project description:Fecal immunochemical tests (FIT) detecting hemoglobin in stool are widely used for non-invasive colorectal cancer (CRC) screening, but their sensitivity leaves room for improvement. Our aim is to identify novel protein biomarkers in stool that outperform or complement hemoglobin in detecting CRCs and advanced adenomas (AAs). Stool samples (one series of 12 CRCs and 10 controls, and a second series of 81 CRCs, 40 AAs, 43 non-advanced adenomas and 129 controls) were analyzed by mass-spectrometry and searched for human proteins. Classification and regression tree and logistic regression analyses were performed to identify protein combinations that differentiated CRCs and/or AAs from controls. Antibody-based assays for four selected proteins were performed on an independent series of FIT samples (14 CRCs, 16 AAs, 18 non-advanced adenomas and 24 controls) Results: In total, 834 human proteins were identified, of which 29 were significantly enriched in CRCs versus controls in both stool sample series. Combinations of four proteins reached sensitivities of 80% and 45% for detecting CRCs and AAs, at 95% specificity, which was higher than hemoglobin alone.
2020-05-26 | PXD007767 | Pride
Project description:To identify novel hypermethylated genes in colorectal cancer (CRC) and to test their potential application in CRC early diagnosis, we performed a genome-wide screening of 57,723 CpG dinucleotides covering 4,010 genes in paired DNA samples extracted from 3 fresh frozen CRC tissues and their matching non-tumor adjacent tissues from a cohort of 3 CRC patients undergoing curative surgery using MIRA-based microarray. We also validated candidate hypermethylated genes screened by MIRA-based microarray in independent CRC samples using combined bisulfite restriction analysis. A total of 297 CpG dinucleotides in CRC covering 211 genes were found to be hypermethylated in CRC tissues. From these 211 candidate methylated genes, seven novel methylated genes were picked up for validation and three genes were confirmed to be methylated in cancer samples but not in non-cancer samples.We also compared the methylation levels of these three novel hypermethylated genes with those of Vimentin and SEPT9, well-known hypermethylated genes in CRC, and found that methylated PHOX2B, FGF12 and GAD2 were better than methylated Vimentin and SEPT9 in differentiating CRC cancer tissue from normal tissue. Significant enrichment analysis of GO terms of the hypermethylated genes showed that a high proportion of hypermethylated genes in tumor tissues are involved in regulation of transcription. Paired experiments, colorectal cancer tissue vs. adjacent non-cancer tissue. Biological replicates: 3 cancer replicates, 3 paired non-cancer replicates.
2011-11-14 | E-GEOD-33545 | biostudies-arrayexpress
Project description:Dysbiotic configurations of the human gut microbiota have been linked with colorectal cancer (CRC). Human small non-coding RNAs are also implicated in CRC and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis but their role is less explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens of patients with CRC, or adenomas, and healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We reported a considerable overlap and correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. Furthermore, we identified a combined predictive signature composed by 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC from healthy and adenoma samples (AUC= 0.87). In summary we reported evidence that host-microbiome dysbiosis in CRC can be observed also by altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more accurate tools for diagnostic purposes.
2019-08-30 | GSE132236 | GEO
Project description:Colorectal cancer (CRC) is a leading cause of cancer death in the United States. Screening for CRC reduces CRC mortality, yet rates of screening in the United States remain low. Fecal occult blood testing (FOBT) has an established positive balance of benefit and risk, is the least expensive, and is the preferred method for nearly half of patients. A newer fecal screening test, the fecal immunochemical test (FIT), offers significant improvements over the FOBT. It is easier to use and is more sensitive at detecting both CRC and precancerous adenomas than the FOBT. The OC-Micro FIT is of particular interest because it is highly sensitive and specific and it is the only FIT test approved in the US that can be processed in an automated manner. Thus, the OC-Micro is an optimal method for use in mass screening programs to improve community CRC-screening rates. However, prior studies of OC-Micro suffer from several limitations: they were conducted in populations not optimal for assessing screening performance in average risk patients in the U.S. and the studies did not clearly establish optimal number of samples required and cut-points for test positivity. Therefore, the overall goal of MY-FIT is to capitalize on the highly integrated and extensive electronic medical record system of the study site to collect two separate sets of data that, when synthesized, will provide a thorough picture of the comparative patient adherence to, sensitivity, specificity, and costs of different protocols for using the OC-Micro FIT. Specifically, among KPNW members aged 50-75 who are at average risk for colorectal cancer (CRC) and who are due for CRC screening (n=78,000), the investigators propose to:
1. Compare the sensitivity, specificity, positive predictive value, and negative predictive value for colorectal cancer and advanced adenoma (advanced neoplasia) between a single-sample FIT (1-FIT) and a two-sample FIT (2-FIT) using varying cut points for a positive test (n=2100).
2. Compare patient adherence to completion of a 1-FIT versus a 2-FIT protocol (n=3000).
3. Assess and compare cost per screen for a 1-FIT versus a 2-FIT protocol, and the cost per advanced neoplasia detected in a 1-FIT versus a 2-FIT protocol (using varying cut points for a positive test) (n=78,000).
Answering the above questions will provide a much-needed strong evidence base for a best-practice, cost-effective method of using the OC-Micro FIT to screen for CRC in a general U.S. population.
| 2128078 | ecrin-mdr-crc
Project description:Phenylacetaldehyde (PAA), a product of phenylalanine metabolism, is catabolized by microbiota and has demonstrated anticancer properties in breast cancer. As intestinal homeostasis is influenced by gut microbiome, we investigated the effect of PAA on colorectal cancer (CRC). In the study, we interrogated the mechanistic pathways induced by PAA treatment using RNA sequencing.
2023-07-11 | GSE207618 | GEO