2d047c60-1dec-43a7-a1ec-eb012ab0ceea - samples
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ABSTRACT:
PROVIDER: EGAD00001011323 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains 44 samples derived from RNA-sequencing data of bile duct and CCA cell lines. Data was generated on Illumina NovaSeq 6000 device in paired-end mode and is stored in compressed FASTQ file format.
| EGAD00001011325 | EGA
Project description:The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains whole exome sequencing data of 37 tumor/normal pairs from the screening cohort plus an additional relapse tumor of one of those 37 patients. Data was generated on Illumina HiSeq 2000 device in paired-end mode and is stored in BAM file format.
| EGAD00001011324 | EGA
Project description:The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains fusion gene analysis using multiplex single primer extension-based RNA-sequencing for a subset of 25 patients of the screening cohort. Data was generated on Illumina NexSeq 550 device in paired-end mode and is stored in compressed FASTQ file format.
| EGAD00001011326 | EGA
Project description:The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains SNP array data for tumor/normal pairs for a subset of 36 patients from the screening cohort plus an additional relapse tumor of one of those 36 patients. Data was generated on a OmniExpress-24 v1.1 Bead Array (Illumina) and is stored in IDAT file format.
| EGAD00010002597 | EGA
Project description:The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains expression array data for 32 patients of the screening cohort with 8 of them having paired normal tissue plus an additional relapse tumor/normal pair of one of those 8 patients and a patient only with normal tissue. Data was generated on a HumanHT-12 v4 Bead Array (Illumina) and is stored in IDAT file format.
| EGAD00010002596 | EGA
Project description:Cholangiocarcinoma (CCA) is a type of highly aggressive cancer arising from the biliary system. Through serum exosome miRNA sequencing, we screened out the differentially expressed miRNA in patients with cholangiocarcinoma(CCA) and common bile duct stones(CBDS).
2022-10-20 | GSE215448 | GEO
Project description:Intrahepatic cholangiocarcinoma (ICC) is a lethal cancer arising from intrahepatic bile ducts in the liver. In the intraductal growth (IDG) type, also referred to as intraductal papillary neoplasm of the bile duct (IPNB), a rare subtype of ICC, cancer cells originating within the bile duct usually invade and infiltrate the nearby liver tissues, resulting in local invasion. IPNB can serve as a good disease model to study the mechanism of local invasion, which is the earliest step of metastasis. Here, we aimed to identify the genes associated with local invasion by comparing the somatic mutations of the matched IPNB tissues with and without local invasion from a set of 11 patients using the Ion AmpliSeq Comprehensive Cancer Panel. Somatic mutation profiling analysis identified RNF213 as a potential candidate gene associated with local invasion in ICC patients. We established stable RNF213-knockdown and shControl cholangiocarcinoma (CCA) cell lines (HuCCT1, YSCCC, and KKU-100). Next, the expression profiling of the RNF213-knockdown and shContol CCA cell lines was analyzed by RNA sequencing.
2024-07-24 | GSE235891 | GEO
Project description:Background: Cholangiocarcinoma (CCA) is a high malignancy, rapid progression tumor of bile duct. Due to its chemoresistance, it always has an extremely poor prognosis. Therefore, it is still need to detailed elucidation the mechanisms of chemoresistance and find the therapeutic targets. Methods: We analysis the expression of MBD2 in CCA and normal bile duct tissues through public database and immunohistochemical (IHC). The role of MBD2 in CCA cells’ proliferation, migration, chemoresistance ability was validated through CCK-8, plate clone assay, wound healing assay, xenograft mice models. Besides, we construct a primary CCA mice model to further confirm the effect of MBD2. RNA-seq, co-IP-MS were used to find the mechanisms of MBD2 leading to chemoresistance. Results: MBD2 is up-regulated in CCA. It could promote the proliferation, migration and chemoresistance of CCA cells. Mechanistically, MBD2 could directly interact with WDR5, and binding to the promoter of ABCB1, then promote the tri-methylation of H3K4 in this region through KMT2A, active the expression of ABCB1. Knocking down of WDR5 or KMT2A could block the transcriptional activation of ABCB1 by MBD2. MM-102 is a molecular inhibitor that targets the interaction of WDR5 with KMT2A. MM-102 could inhibit the expression of ABCB1 in CCA cells, and decrease the chemoresistance of CCA to cisplatin. Conclusion: MBD2 promote the progress and chemoresistance of CCA through interact with WDR5. MM-102 could effectively block this procedure and enhance the sensitivity to cisplatin of CCA.
2024-09-30 | GSE275477 | GEO
Project description:Assays in bile duct cancer patients showed 984 CNVs in 306 CNV regions (CNVR) distributed throughout all 22 chromosomes. Bile duct cancer patients had a mean of 21.8 gains and 19.2 losses of genes, with an average of 35.9 CNVRs per patient. Frequent sites of gains were at chromosomes 22q11.22, 2p11.2-p.11.1, 14q32.33 and 17q12, whereas frequent sites of losses were at 19q12-q13.43. Investigation of CNV in 24 bile duct cancer tissue samples
2013-07-13 | E-GEOD-48835 | biostudies-arrayexpress
Project description:Introduction: Accurate diagnosis of distal cholangiocarcinoma (CCA) and pancreatic ductal adenocarcinoma (PDAC) is a challenge with clinical consequences. Both are lethal malignancies with distinct therapeutic options. This study aimed to identify a circulating microRNA (miRNA) signature to diagnose and discriminate distal CCA from PDAC. Methods: In the discovery phase, microarray profiling of 752 miRNAs was performed on plasma samples of seven patients with distal CCA and seven age- and sex-matched healthy controls. Significant candidate miRNAs were selected for validation based on predefined selection criteria. In the validation phase, these miRNAs were analyzed by RT-qPCR in an independent cohort of healthy controls (n=32), benign periampullary disease (n=20), distal CCA (n=24), and age- sex- and stage-matched PDAC (n=24). Data were normalized to a combination of two reference genes. The optimal diagnostic combination of miRNAs was determined by logistic regression. Sensitivity and specificity were evaluated by ROC curves and AUC values. Results: In the discovery phase, 19 miRNAs were significantly deregulated in patients with distal CCA compared to healthy controls. In the validation phase, 12 candidate miRNAs were selected for validation by RT-qPCR based on pre-defined selection criteria. A two-miRNA panel of downregulated miR-16 and upregulated miR-877 was able accurately distinguish distal CCA from benign disease as well as from PDAC. Conclusion: This is the first study to identify a combined panel of plasma miRNAs which shows promising diagnostic capability to serve as distal CCA signature with the potential to discriminate distal CCA from PDAC.
2019-11-26 | GSE117687 | GEO