Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA280866 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:SNP-array profiling of 21 novel primary and metastatic colorectal cancer cell lines [Illumina HumanExome-12 v1.0 BeadChip]
| PRJNA280868 | ENA
Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for three human ES cell lines, namely, SEES-1, SEES-2, and SEES-3. Samples were collected after 4 to 60 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher genomic stability of the ES cells compared to some well-known normal cell lines.
2015-05-20 | GSE54576 | GEO
Project description:To look at genes/pathways differentially expressed in metastatic and primary tumor cells we performed global gene expression profiling of the 3 sets of HNSCC lines derived from primary tumors and matched metastatic sites. Illumina HT-12 v4 BeadChip arrays were used. The data suggest that HNSCC lines derived from metastatic sites exhibit phenotypes distinct from those found in cells derived from the corresponding primary tumors. Metastatic cell lines upregulated several pathways involved in stem cell self-renewal, invasion and migration, which are well known characteristics of metastatic progression. We conclude that the cell lines derived from primary patient tumors and matched metastatic sites represent a reliable model to study HNSCC metastasis.
2018-07-27 | GSE117753 | GEO
Project description:Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance. Results: DNA copy-number alterations (CNA) were compared between primary and metastasis derived cell lines. In concordance with previous studies copy-number gain of chr20, and loss of chr8p were found highly specific for liver metastases. Previously reported BRAF-mutation associated DNA methylation profiles could be validated on the genome-wide DNA methylation profiles of these cell lines. 47.6% of the loci previously reported to associate with BRAF mutation status were reproduced in this dataset. When examining the gene expression profiles in conjunction with these DNA methylation results, we identified 20 genes of which the gene expression correlated with the DNA methylation status, including MEIS1, LRAT and STC2. These genes have previously been reported to be subject to transcriptional regulation through DNA hypermethylation, validating our approach. Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. SNP-array analysis of 21 novel CRC cell lines; 16 with Illumina HumanExome-12 v1.2 BeadChip and 5 with Illumina HumanExome-12 v1.0 BeadChip.
2016-02-29 | E-GEOD-67773 | biostudies-arrayexpress
Project description:Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance. Results: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. SNP-array analysis of 21 novel CRC cell lines; 16 with Illumina HumanExome-12 v1.2 BeadChip and 5 with Illumina HumanExome-12 v1.0.
2016-02-29 | E-GEOD-67774 | biostudies-arrayexpress
Project description:Analysis of two metastatic OS cell lines, KHOS and KRIB, and two non-metastatic OS cell lines, HOS and U2OS. Results show differences in gene expression between cell lines with different ability to metastasise in vivo. Each of the four cell lines were analyzed in tripicate. Total RNA was extracted from each triplicate cell line culture with Trizol. cRNA was amplified using the Ambion Illumina Total Prep RNA Amplification Kit. Concentration was determined in NanoDrop and qulity checked in the Agilent Bioanalyzer, before hybridizing to Illumina HT-12 BeadChip Array.
2013-07-19 | E-GEOD-49003 | biostudies-arrayexpress
Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for iPS cells derived from xeroderma pigmentosum patients (XP3OS, XP40OS, and XPEMB-1). Samples were collected after 10 to 25 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher mutation rate of the iPS cells compared to those from normal cells.
2015-06-24 | GSE55520 | GEO
Project description:Melanoma cell lines were genotyped to evaluate copy number differences between nodular melanoma (NM) and superficial spreading melanoma (SSM). Cell lines were also evaluated for copy number alterations in the SKP2/p27 axis. Affymetrix SNP arrays were performed according to manufacturer's instructions using DNA extracted from 18 melanoma cell lines and 4 melanocyte controls. Affymetrix SNP6.0 Array data for melanoma cell lines Copy number analysis of Affymetrix SNP 6.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP) that were used to construct the baseline for copy number analysis.
2010-10-21 | E-GEOD-22305 | biostudies-arrayexpress
Project description:Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. We analyzed hiPSC line and genetically modified derivatives using high-density SNP array to investigate genomic instability associated reprogramming and genetic modification. Primary iPSC lines derived from patients with alpha-1 antitrypsin deficiency were generated. This genetic disorder is caused by homozygous mutation (Glu342Lys) in the SERPINA1 gene. We carried out mutation correction by 2 steps: zinc-finger nuclease-stimuated gene targeting and piggyBac trasnsposon-mediated selection cassette elimination. Parental fibroblast lines, primary iPSC lines and homozygously targeted iPSC lines were subjected to SNP genotyping using Illumina CytoSNP-12 BeadChiP.
2011-08-31 | E-GEOD-31035 | biostudies-arrayexpress