Paired human colon and tumor biopsies
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA808084 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Paired human colon and tumor biopsies were obtained and made into single cell suspensions. Cells were encapsulated into droplets and libraries prepared using the 10X Genomics platform and libraries sequenced on an Illumina NextSeq
2022-02-21 | GSE196964 | GEO
Project description:24 colon normal and tumor pairs using Illumina BeadChip Human Ref8-v2. Genetic and epigenetic defects in Wnt/ß-catenin signaling play important roles in colorectal cancer progression. Here we identify DACT3, a member of the DACT (Dpr/Frodo) gene family, as a negative regulator of Wnt/ß-catenin signaling that is transcriptionally repressed in colorectal cancer. Unlike other Wnt signaling inhibitors that are silenced by DNA methylation, DACT3 repression is associated with bivalent histone modifications. Remarkably, DACT3 expression can be robustly de-repressed by a pharmacological combination that simultaneously targets both histone methylation and deacetylation, leading to strong inhibition of Dishevelled (Dvl)-mediated Wnt/ß-catenin signaling and massive apoptosis of colorectal cancer cells. Our study identifies DACT3 as an important regulator of Wnt/ß-catenin signaling in colorectal cancer and suggests a potential strategy for therapeutic control of Wnt/ß-catenin signaling in colorectal cancer. The clinical information for the colon tumor is not available. Keywords: human colon tumor
2008-03-29 | GSE10950 | GEO
Project description:We applied tandem mass spectrometry, data search, and bioinformatics to investigate the taxonomic composition and functional annotations of cultivated gut microbiomes derived from clinical colon biopsies
2024-11-01 | PXD047418 | Pride
Project description:Clinical proteomics research is in part limited by the availability of clinical samples. However, large biobanks exist worldwide containing formalin-fixed and paraffin embedded samples and samples stored in RNAlater. The extraction of proteins for proteome analysis from samples prepared by either method has been demonstrated. However, the impact of the preservation method on the result of a quantitative proteome analysis remains largely uninvestigated. We, therefore, conducted a proteome analysis of human colon mucosal biopsies where the material had been preserved accordingly. Twenty-four colon mucosal biopsies were extracted from the sigmoideum by endoscopy from two participants. The biopsies were either directly-frozen, stabilized in RNAlater, or stabilized by formaldehyde fixation immediately or incubated for 30 min to simulate a clinical situation, followed by paraffin embedding. The impact of the preservation method on the result of a proteome analysis was characterized by high throughput gel free quantitative proteomics.
2015-11-23 | PXD002029 | Pride
Project description:We compared the expression of microRNAs in primary colon tumors with their paired liver metastases using the Nanostring human microRNA assays version 1 23 microRNAs were found to be differentially expressed between colon primary tumors and their paired metastases
2014-08-01 | GSE44121 | GEO
Project description:The goal of this study was to identify microRNAs that were differentially expressed in colon tumors and determine if microRNA expression profiles could predict poor cancer survival. Keywords: disease state design For these experiments, we used RNA extracted from pairs of colon adenocarcinoma tissue and adjacent nontumorous tissue. RNA from pairs of tissues were hybridized on the same day with up to 12 pairs of tissues being hybridized on a given day. To identify differentially expressed microRNAs, paired class comparison in BRB array tools was used. Samples were paired in the individual from where the tissues originated. Therefore, every tumor tissue has it's own nontumorous reference for comparison.
2008-02-12 | E-GEOD-7828 | biostudies-arrayexpress
Project description:Gene expression profiles of paired normal adjacent mucosa and tumor samples from 98 individuals and 50 healthy colon mucosae, were obtained through Affymetrix Human Genome U219 Arrays. This dataset is in the context of the COLONOMICS project and to query additional information you can visit the project website www.colonomics.org. Colon tumor and adjacent paired normal mucosa tissues samples used in this study were selected from a series of cases with a new diagnosis of colorectal adenocarcinoma histologically confirmed. Included cases were from a homogenous series of patients with more than three years of follow up, early stage (II), without neoadjuvant chemotherapy and microsatellite stable colon cancer. Additionally, samples of colon mucosa from 50 healthy donors without colonic lesions were obtained during colonoscopy.
2014-03-14 | E-GEOD-44076 | biostudies-arrayexpress
Project description:To investigate lncRNA expression in colon cancer cells in comparison with paired normal colon epithelial cells by use of lncRNA microarray.
2018-07-29 | GSE117830 | GEO
Project description:We compared the expression of microRNAs in primary colon tumors with their paired liver metastases using the Nanostring human microRNA assays version 1 23 microRNAs were found to be differentially expressed between colon primary tumors and their paired metastases Total mRNA was extracted from flash frozen primary colon tumors and paired metastases. 18 tissues from 9 donors were used for this study. 100 ng of RNA was hybridized to Nanostring Human 0microRNA assays version 1.0. Data was normalized according to manufacterer's recommendation. This included background substraction and normalizing to the geometric mean of the highest 75 microRNAs.
2014-08-01 | E-GEOD-44121 | biostudies-arrayexpress
Project description:Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors. Study aims to survey and analyze variation from disease in different GI regions. Keywords: disease state analysis
2008-06-17 | GSE11223 | GEO