The ImmgenT Open-Source project
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1262504 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-05-14 | GSE297097 | GEO
Project description:Data in support of the manuscript "Open-source electrophilic fragment screening platform for UCHL1 covalent inhibitors"
2024-12-06 | MSV000096608 | MassIVE
Project description:This experiment captures the baseline expression of 6 cell lines (K562, KU812, MEG01, HEL9217, F36-P, UT7) selected for Project 1, Open Targets 020. These cell lines are all possible cell models for haematopoiesis.<br>This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalized cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.
2016-01-27 | E-MTAB-4101 | biostudies-arrayexpress
Project description:Paper title: Adding Open Spectral Data to MassBank and PubChem using Open Source Tools to Support Non-Targeted Exposomics of Mixtures
Author List: Anjana Elapavalore, Todor Kondic, Randolph R. Singh, Benjamin A. Shoemaker, Paul A. Thiessen, Jian Zhang, Evan E. Bolton, Emma L. Schymanski
Brief description of the data submitted: RAW Files and peak list files used in this workflow to generate open source spectral records. Supplementary files contain the resulting output CSV files.
2023-04-20 | MSV000091754 | GNPS
Project description:<p>MAVEN, an open-source software program for analysis of LC-MS metabolomics data, was originally released in 2010. As mass spectrometry has advanced in the intervening years, MAVEN has been periodically updated to reflect this advancement. This manuscript describes a major update to the program, MAVEN2, which supports LC-MS/MS analysis of metabolomics and lipidomics samples. We have developed algorithms to support MS/MS spectral matching and efficient search of large-scale fragmentation libraries. We explore the ability of our approach to separate authentic from spurious metabolite identifications using a set of standards spiked into water and yeast backgrounds. To support our improved lipid identification workflow, we introduce a novel <em>in-silico</em> lipidomics library covering major lipid classes and compare searches using our novel library to searches with existing <em>in-silico</em> lipidomics libraries. MAVEN2 source code and cross-platform application installers are freely available for download from GitHub under a GNU permissive license [ver 3], as are the in silico lipidomics libraries and corresponding code repository.</p>
2024-07-22 | MTBLS3097 | MetaboLights
Project description:Human iPSC and macrophages derived from them are increasingly popular tools for research into both infectious and degenerative diseases. However, as the field strives for greater modelling accuracy, it is becoming ever more challenging to justify the use of undefined and proprietary media for the culture of these cells. We describe here a defined, serum-free, open-source medium for the differentiation of iPSC-derived macrophages. This medium is equally capable of maintaining these cells compared to commercial alternatives. The macrophages differentiated in this medium display improved terminally differentiated cell characteristics, reduced basal expression of induced anti-viral response genes, and improved polarisation capacity. We conclude that cells cultured in this medium are an appropriate and malleable model for tissue resident macrophages, on which future differentiation techniques can be built.
2021-04-02 | GSE171313 | GEO
Project description:This experiment captures the baseline expression of two cell lines (A549, BEAS-2B) selected for Project 3, Open Targets 020 (http://opentargets.org). These cell lines are both possible models for lung disease. In addition, the baseline expression of bronchial epithelial primary cells (NHBE cells) from 3 donors has also been measured. <br> This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalized cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.
2017-07-04 | E-MTAB-4729 | biostudies-arrayexpress
Project description:This submission contains human protein interaction datasets of four proteins (BCL2, TDP-43, MDM2, PTEN) across three cancer cell lines (G401, T47D, A375) and one iPSC-derived neuronal cell line (glutamatergic patterned induced neuron, GPiN). The data were generated to demonstrate the utility of Genoppi (lagelab.org/genoppi), an open-source computational tool that enables integration of quantitative proteomic results with genetic data. Our analyses show a general pattern of both cell-type-independent and cell-type-specific interactions for the tested proteins. In particular, our results suggest that the neuron-specific interactions of BCL2 and TDP-43 are mediating their genetic involvement in amyotrophic lateral sclerosis.
2021-02-10 | PXD022667 | Pride
Project description:The aim of this experiment was to characterize the gene expression of two common immortalized T cell lines (HUT78 and JURKAT E6.1) with and without activating stimuli. Two independent cultures were carried out for each of the cell lines. Cells were cultured according to supplier recommendations and either left untreated or stimulated with Dynabeads human T-activator CD4/CD28 beads (Invitrogen, UK) at a ratio of 1 bead:3 cells for 48 hours. This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalised cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.
2018-06-11 | E-MTAB-6869 | biostudies-arrayexpress