EGAS00001000728-sc-20140723 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001000894 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.
| EGAS00001000728 | EGA
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2021-04-12 | GSE157017 | GEO
Project description:The glucocorticoid receptor (GR) regulates adaptive transcriptional programs that alter metabolism in response to stress. Network properties that allow GR to tune gene expression to match specific physiologic demands are poorly understood. We analyzed the transcriptional consequences of GR activation in murine lungs deficient for Klf15, a transcriptional regulator of amino acid metabolism that is induced by glucocorticoids and fasting
2013-05-13 | GSE44695 | GEO
Project description:Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). These results show high (R2 >0.9) intra-platform consistency across test sites, high inter-platform concordance (R2 >0.8) for transcriptome profiling, and a large set of novel splice junctions observed across all platforms. Also, we observe that protocols using ribosomal RNA depletion can both salvage degraded RNA samples and also be readily compared to polyA-enriched fractions. These data provide a broad foundation for standardization, evaluation and improvement of RNA-seq methods. Two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS).
2014-05-14 | E-GEOD-46876 | biostudies-arrayexpress
Project description:Genetic screens using CRISPR technology are widely exploited to explore novel targets and discover resistance mechanisms of cancer treatments, including cancer immunotherapy. As it is a time- and resource-intensive manner to individually validate potential candidates and clarify their working mechanisms, single-cell CRISPR screen platforms are designed and developed to parallelly characterize these factors and explore underlying mechanisms in a high-throughput manner. By leveraging the resources generated in our previous studies, Perturb-seq featured with capture sequences integrated into gRNA-expressing vectors and CROP-seq featured with poly(A)-tailed gRNA transcripts under the control of RNAPII promoters were selected among several independent single-cell CRISPR screen platforms to directly evaluate the performance of different scCRISPR screen platforms in determining underlying mechanisms of tumor intrinsic immune regulation and optimize experimental conditions and data analysis in immune-related scCRISPR screens. In the study, the influence of each perturbation on the gene expression profile and the response to in vitro T cell killing and in vivo anti-PD-1 treatment were comprehensively appraised at the single-cell level. It is clearly demonstrated that scCRISPR screen platforms could efficiently characterize gene expression profiles and perturbation effects present in individual cells during both in vitro and in vivo immune-related screen processes. Particularly, scCRISPR screen platforms presented more detail to determine heterogeneous change of gene expression in distinct knockout tumor cells in the presence of immune attack which cannot be easily assessed by canonical bulk RNA-seq. Collectively, scCRISPR screen technologies provide scalable and reliable platforms to validate identified tumor intrinsic immune factors identified from genome-wide CRISPR screens and elucidate their potential working mechanisms.
2022-11-13 | GSE206107 | GEO
Project description:A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent
2007-09-14 | GSE8994 | GEO
Project description:Ongoing progress in high-throughput next-generation sequencing (NGS) has enabled clinicians to comprehensively characterize the genomic landscape of tumors, guide treatment decisions, and facilitate clinical trial enrollment. The role of liquid NGS in anaplastic thyroid carcinoma (ATC) remains unclear, particularly in cases where tissue NGS is not feasible or yields inadequate results. Among these, 26 patients had adequate tissue for commercially available tissue NGS (ACTOnco®+, 440 genes), 15 had access to a commercially available liquid NGS platform (ACTMonitor®+, 50 genes), and 13 patients underwent both tissue and liquid NGS. The genetic alterations observed in ATC exhibited a high degree of heterogeneity, involving several pathways, including RAS/RAF/MEK/ERK, PI3K/AKT/mTOR, cell cycle regulation, other receptor tyrosine kinases, DNA damage response, DNA mismatch repair (MMR, 34.6%, including MLH1, MSH6, MSH2, and PMS1), and chromatin remodeling. The most frequently mutated genes in tissue NGS were TP53 (17/26, 65.4%) and BRAF (8/26, 30.8%). Among the 13 pairs analyzed on both platforms, the concordance rates were 84.6% and 69.2% for BRAF and TP53, respectively. Among two patients without sufficient tissue for NGS, liquid NGS provided additional information on genetic alterations. NGS platforms, whether applied to tissue or liquid samples, can empower clinicians to identify targetable oncogenic events in ATC. Liquid biopsy provides supplementary information when the tissue is insufficient for NGS.
2025-01-11 | GSE281660 | GEO
Project description:The glucocorticoid receptor (GR) regulates adaptive transcriptional programs that alter metabolism in response to stress. Network properties that allow GR to tune gene expression to match specific physiologic demands are poorly understood. We analyzed the transcriptional consequences of GR activation in murine lungs deficient for Klf15, a transcriptional regulator of amino acid metabolism that is induced by glucocorticoids and fasting Wild type and Klf15 KO mice were treated with dexamethsone or saline control for 4 and 8 hours.
2013-05-13 | E-GEOD-44695 | biostudies-arrayexpress
Project description:Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). These results show high (R2 >0.9) intra-platform consistency across test sites, high inter-platform concordance (R2 >0.8) for transcriptome profiling, and a large set of novel splice junctions observed across all platforms. Also, we observe that protocols using ribosomal RNA depletion can both salvage degraded RNA samples and also be readily compared to polyA-enriched fractions. These data provide a broad foundation for standardization, evaluation and improvement of RNA-seq methods. Two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). Please note that the samples were named following the ABRF-Platform-Site-Sample-Replicate# format. For example, ABRF-454-CNL-A-1 means Sample A was run on 454 platform at Cornell and this is the first replicate, and ABRF-454-CNL-A-2 means the same exact sample was ran with same machine at same location and is 2nd replicate.
2014-05-14 | E-GEOD-48032 | biostudies-arrayexpress