Ontology highlight
ABSTRACT:
PROVIDER: PRJNA912635 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22750159_1.fastq.gz | Fastqsanger.gz | |||
| SRR22750159_2.fastq.gz | Fastqsanger.gz | |||
| SRR22750160_1.fastq.gz | Fastqsanger.gz | |||
| SRR22750160_2.fastq.gz | Fastqsanger.gz | |||
| SRR22750161_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:We investigated the CNAs in a four stage tumorigenesis model. This model included copy number analyses in non-transgenic NMRI mice (normal) and in transgenic SVT/t mice: non-malignant hyperplastic mammary glands and breast cancers, as well as breast cancer derived cell lines. We focused our research on copy number analyses to compare the genomic alterations that occur during tumorigenesis. We addressed the question, whether common predisposed chromosomal breakpoints could be seen to promote malignant transformation. We can report a characteristic increase of copy number alterations from normal to tumor stage in our model. Furthermore, we have identified chromosomal segments and found characteristic fragmentations.
2012-09-04 | GSE35873 | GEO
Project description:Exon-Level and Gene-Level Expression analysis of Tumor and Normal Samples The effect of somatic copy number alterations at the functional level can be analyzed by looking into the expression pattern of the affected genes. The task of identifying the ‘affected’ genes is facilitated by robust algorithms that carry out sensitive and confident localization of the targets of somatic copy number alterations in cancer. We had earlier identified 144 genes by GISTIC analysis that were potential targets of SCNAs. In this study we report our findings based on exon level analysis of these genes. Only a subset of these genes was found to have significant changes in expression levels. 8/24 genes were found to have fold change value >1.5 and 3 of them were reported as novel in their association with CRC. The splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumor samples. Causal network analysis was carried out to study the difference in patterns of target genes affected by transcription factors identified by the GISTIC analysis. LIMMA analysis was carried out to find differentially expressed genes and their functional significance was studied using ingenuity pathway analysis.
2014-09-01 | GSE50421 | GEO
Project description:Interventions: Group 1: Blood and sputum samples as well as paraffin embedded tumour tissue from patients with microsatellite stable colorectal cancer shall be analysed before therapy and over time to establish and validate hotspot mutation and somatic copy number variant (SCNAs) analysis. We therefore need the following samples:
- Two Cell-Free DNA BCT CE Streck tubes with 8 ml blood per sampling for preparation of plasma-DNA.
- One sputum tube (only at study inclusion).
- FFPE tissue samples from the primary tumor (from initial surgery)
Group 2: Blood samples of tumor-free control persons shall be tested for hotspot mutations and somatic copy number variants (SCNAs) to identify technical artefacts and improve our protocols. We therefore need the following samples:
- Two Cell-Free DNA BCT CE Streck tubes with 8 ml blood per sampling for preparation of plasma-DNA.
Primary outcome(s): Identification of tumorspecific SCNAs in plasma samples of colorectal cancer patients
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: other
| 2433407 | ecrin-mdr-crc
Project description:Somatic copy number variants in monozygotic twins and elderly single-born individuals
| PRJNA151185 | ENA
Project description:Exon-Level and Gene-Level Expression analysis of Tumor and Normal Samples The effect of somatic copy number alterations at the functional level can be analyzed by looking into the expression pattern of the affected genes. The task of identifying the M-bM-^@M-^XaffectedM-bM-^@M-^Y genes is facilitated by robust algorithms that carry out sensitive and confident localization of the targets of somatic copy number alterations in cancer. We had earlier identified 144 genes by GISTIC analysis that were potential targets of SCNAs. In this study we report our findings based on exon level analysis of these genes. Only a subset of these genes was found to have significant changes in expression levels. 8/24 genes were found to have fold change value >1.5 and 3 of them were reported as novel in their association with CRC. The splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumor samples. Causal network analysis was carried out to study the difference in patterns of target genes affected by transcription factors identified by the GISTIC analysis. LIMMA analysis was carried out to find differentially expressed genes and their functional significance was studied using ingenuity pathway analysis. We conducted a group-wise comparison of Tumor vs Normal samples obtained from cancer patients. Array data was processed using Expression Console and AltAnalyze
2014-09-01 | E-GEOD-50421 | biostudies-arrayexpress
Project description:We examined the effects of hydroxyurea (HU) treatment on germline copy number variants (CNVs) in vivo in male mice. Several trials of HU administration were performed by oral gavage and subcutaneous pump, with CNVs characterized in C57BL/6 x C3H/HeJ hybrid mouse offspring by microarray and mate-pair sequencing. This accession contains the Nimblegen aCGH microarray data from mice treated by oral gavage or by subcutaneous pump.
2019-05-08 | GSE114754 | GEO
Project description:Identification of copy number variants in horses
| PRJNA146995 | ENA
Project description:Identification of Copy Number Variants in Dogs
| PRJNA153385 | ENA