Similar Datasets
Project description:Jurkat clone E6-1 is a human T-cell line derived from a paediatric case of acute leukaemia, and is frequently employed as a model T-cell for immunology research. In this study, we characterised genomic, transcriptomic, and functional features of Jurkat clone E6-1 cells stored in three different laboratories, and compared these to Jurkat E6-1 cells from the ATCC. Jurkat clone E6-1 populations were first karyotyped, which results showing marked cytogenomic heterogeneity between cell line. These results were confirmed through chromosomal microarray analysis. Whole exome sequencing was then conducted on each cell line, and revealed distinct mutational profiles between populations. Mutational differences between Jurkat clone E6-1 populations detected by cytogenomic approaches and whole exome sequencing led to divergent transcriptomic profiles identified by bulk RNA sequencing, which, in turn, impacted cellular phenotype and function shown by flow cytometry and multiplex cytokine bead array data. Overall, we found substantial genomic heterogeneity between and within Jurkat clone E6-1 cells, resulting in significant differences in gene expression and function. This research highlights the extreme genomic instability of Jurkat clone E6-1 cells, the importance of monitoring cell passage number and procuring fresh cell line stocks, and the value of multi-omic approaches to characterise cell lines to improve the accuracy, reproducibility, and translatability of research.
2025-04-08 | GSE263543 | GEO
Project description:Coloboma is a developmental eye disorder characterised by failure of epithelial fusion during optic fissure closure (OFC). The incomplete identification of genes and molecular pathways that directly regulate fusion restricts current understanding of OFC mechanisms and coloboma causation. The recent identification of pioneer cells at the edges of the fissure margins provides an opportunity to molecularly characterise OFC. Here we describe the generation of a pioneer cell reporter chicken line (NTN1-T2A-eGFP) by targeting green fluorescent protein into the Netrin-1 locus using CRISPR/Cas9 methodology. Our strategy gave 100% transmission of heterozygous (NTN1T2A-eGFP/+) embryos in which GFP localisation faithfully replicated endogenous NTN1 expression. Furthermore, all NTN1T2A-eGFP/+ embryos and hatched birds were phenotypically normal. We then optimised the isolation of GFP expressing cells from embryonic eyes using spectral fluorescence cell-sorting and performed transcriptomic profiling that revealed multiple new pioneer cell markers. Our approach implicated several novel pathways, including HGF/MET signalling, that plausibly mediate fusion in OFC. This work is the first to characterise pioneer cells directly at the molecular level and provides a new chicken reporter line with broad experimental utility.
2025-04-02 | GSE275781 | GEO
Project description:To identify genomic regions which display concordant gene expression in prostate cancer, we performed expression profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP. These expression arrays were integrated ChIP-on-chip studies of active and repressive epigenetic marks in same cells to discover and characterise regions of Long Range Epigenetic Silencing (LRES) in prostate cancer.
2010-01-04 | GSE19725 | GEO
Project description:We optimised a new differentiation paradigm to produce midbrain dopaminergic neurons from hiPSCs. To characterise their identity, we performed scRNA-seq to investigate their gene expression and molecular identity.
2022-10-05 | GSE213569 | GEO
Project description:Among B-cell lymphomas mantle cell lymphoma (MCL) has the worst prognosis. By using a combination of genomic and expression profiling (Affymetrix GeneChip Mapping 10k Xba131 and U133 set), we analysed 26 MCL samples to identify genes relevant to MCL pathogenesis and that could represent new therapeutic targets. Recurrent genomic deletions and gains were detected. Genes were identified as overexpressed in regions of DNA gain on 3q, 6p, 8q, 9q, 16p and 18q, including the cancer genes BCL2 and MYC. Among the transcripts with high correlation between DNA and RNA, we identified SYK, a tyrosine kinase involved in B-cell receptor signalling. SYK was amplified at DNA level, as validated by fluorescence in situ hybridisation (FISH) analysis, and overexpressed at both RNA and protein levels in the JeKo-1 cell line. Low-level amplification, with protein overexpression of Syk was demonstrated by FISH in a small subset of clinical samples. After treatment with low doses of the Syk inhibitor piceatannol, cell proliferation arrest and apoptosis were induced in the cell line overexpressing Syk, while cells expressing low levels of Syk were much less sensitive. A combination of genomic and expression profiling suggested Syk inhibition as a new therapeutic strategy to be explored in lymphomas. Keywords: cell type comparison
2006-02-08 | GSE4176 | GEO
Project description:We have sequenced using single end and paired end sequencing GMPs, CMPs, EoPs, SiglecF+IL5ra- GMPs and eosinophils to be able to characterise this new subset of GMPs and to be able to give it some context within a lineage trajectory analysis
2018-12-03 | GSE107495 | GEO
Project description:We report eight new high-quality genomes of Orientia tsutsugamushi, generated using PacBio single molecule long read sequencing.
| PRJEB24834 | ENA
Project description:Transcriptional profiles of U2 OS cell line treated with ~21 thousands of compounds from diversity-oriented-synthesis (DOS) library.
2014-05-30 | LDS-1194 | LINCS
Project description:Part of a study to characterise the two component regulatory system yehUT of Salmonella enterica serovar Salmonella Typhi and Typhimurium.
2013-09-17 | GSE50825 | GEO
Project description:Various cancers such as colorectal cancer (CRC) are associated with alterations in protein glycosylation. CRC cell lines are frequently used to study these (glyco)biological changes and their mechanisms. However, differences between CRC cell lines with regard to their glycosylation have hitherto been largely neglected. Here, we comprehensively characterized the N-glycan profiles of 25 different CRC cell lines, derived from primary tumors and metastatic sites, in order to investigate their potential as glycobiological tumor model systems and to reveal glycans associated with cell line phenotypes. We applied an optimized, high-throughput membrane-based enzymatic glycan release for small sample amounts. Released glycans were derivatized to stabilize and differentiate between a2,3- and a2,6-linked N-acetylneuraminic acids, followed by N-glycosylation analysis by MALDI-TOF(/TOF)-MS. Our results showed pronounced differences between the N-glycosylation patterns of CRC cell lines. CRC cell line profiles differed from tissue-derived N-glycan profiles with regard to their high-mannose N-glycan content but showed a large overlap for complex type N-glycans, supporting their use as a glycobiological cancer model system. Importantly, we could show that the high-mannose N-glycans did not only occur as intracellular precursors but were also present at the cell surface. The obtained CRC cell line N-glycan features were not clearly correlated with mRNA expression levels of glycosyltransferases, demonstrating the usefulness of performing the structural analysis of glycans. Finally, correlation of CRC cell line glycosylation features with cancer cell markers and phenotypes revealed an association between highly fucosylated glycans and CDX1 and/or villin mRNA expression that both correlate with cell differentiation. Together, our findings provide new insights into CRC-associated glycan changes and setting the basis for more in-depth experiments on glycan function and regulation.
2017-02-03 | MTBLS227 | MetaboLights