2126f067-dc14-4271-9adf-21a30ba15e14 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010273 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:LNPs have been demonstrated to hold great promise for the clinical advancement of RNA therapeutics. Continued exploration of LNPs for application in new disease areas requires identification and optimisation of leads in a high throughput way. Currently available high throughput in vivo screening platforms are well suited to screen for cellular uptake but less so for functional cargo delivery. We report on a platform which measures functional delivery of LNPs using unique peptide ‘barcodes’. We describe the design and selection of the peptide barcodes and the evaluation of these for the screening of LNPs. We show that proteomic analysis of peptide barcodes correlates with quantification and efficacy of barcoded reporter proteins both in vitro and in vivo and, that the ranking of selected LNPs using peptide barcodes in a pool correlates with ranking using alternative methods in groups of animals treated with individual LNPs. We show that this system is sensitive, selective, and capable of reducing the size of an in vivo study by screening up to 10 unique formulations in a single pool, thus accelerating the discovery of new technologies for mRNA delivery.
2024-10-17 | PXD053797 | Pride
Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we assess the RNA-degradation and decay rates by subjecting both spike-in molecules to range of repeated freezing and thawing (freeze-thaw) cycles. We manually add spike-in molecules across a 96-well plate (containing cells and reagents), perform Smart-Seq2 method manually and generate single-cell libraries using Nextera XT kit
2017-03-14 | E-MTAB-5481 | biostudies-arrayexpress
Project description:These are the results of the iCLIP experiment for p62/SQSTM1 in Human Huh-7 cells treated with DMSO. We used iCLIP method to identify the RNA targets of p62 and nucleotide positions of the p62 interaction on RNA. We used 2 replicates and 2 different antibodies against endogenous p62 to enrich protein/RNA complexes. cDNAs were tagged with iCLIP composite barcodes (e.g. NNNTTGTNN) which contain 4 sample-encoding bases (e.g. TTGT) and and 5 random bases (noted with N in NNNTTGTNN example) which serve as unique molecular identifiers to post-filter PCR duplicates. These composite barcodes are found in the read headers (after last colon ':' character) of submitted fastq files.
2018-03-31 | E-MTAB-4894 | biostudies-arrayexpress
Project description:Whole exome sequencing (WES) libraries were prepared from 200ng of genomic DNA using the Agilent SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library coupled with the Agilent SureSelect XT Human all exon v6 capture reagent. Libraries were sequenced on a NextSeq 550 sequencer using the High output 300 cycles kit generating 150bp paired end single-indexed reads. Alignment against b37 using Novoalign (version 3.02.08).
| EGAD00001004539 | EGA
Project description:<p>The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19). </p>
| phs001115 | dbGaP
Project description:Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes
| PRJNA381100 | ENA
Project description:Detecting strain-specific barcodes with mass spectrometry can facilitate the screening of genetically engineered bacterial libraries. Here, we introduce intact protein barcoding, a method to measure protein-based library barcodes and metabolites using flow-injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin with N-terminal tags of six amino acids. We demonstrate that FI-MS detects intact ubiquitin proteins and identifies the mass of N-terminal barcodes. In the same analysis, we measured relative concentrations of primary metabolites. We constructed 6 ubiquitin-barcoded CRISPRi strains targeting metabolic enzymes, and analyzed their metabolic profiles and ubiquitin barcodes. FI-MS detected barcodes and distinct metabolome changes in CRISPRi-targeted pathways. We demonstrate the scalability of intact protein barcoding by measuring 132 ubiquitin barcodes in microtiter plates. These results show that intact protein barcoding enables fast and simultaneous detection of library barcodes and intracellular metabolites, opening up new possibilities for mass spectrometry-based barcoding.
2024-10-30 | MSV000096254 | MassIVE
Project description:To facilitate scalable longitudinal profiling of single cells we developed a universal permanent genetic cell barcoding technology based on the expression of shielded small nucleotides coupled with single-cell RNA-seq (SSN-seq). SSN barcodes are highly expressed and contain direct-capture sequences to enable recovery of distinct barcodes directly in each single-cell transcriptome allowing cell identity history to be recorded over time, in parallel with cell identity. SSN-seq is compatible with both 3’ and 5’ single-cell profiling and is readily adaptable to numerous cell types including human primary T cells and CAR T cells making it a promising tool for rapidly improving adoptive cell therapies and expanding their functionality. We applied SSN-seq to track the dynamics of CAR T cell states at the time of infusion and upon isolation from in vivo tumor rechallenge model. Our study identified that a novel combination of cytokines and small molecule inhibitors used for CAR T cells manufactured ex vivo, promotes the expansion of persistent CD4+ memory T cell populations in vivo. Together, these results demonstrate the utility of our method for multiplexed perturbation experiments that reveal the dynamics of cell states over time, with a high degree of confidence.
2023-07-31 | GSE201647 | GEO
Project description:single cell RNA Sequencing runs for various models linking transcriptomes with regional position using spatially printed barcodes
2020-06-01 | GSE145502 | GEO
Project description:More then 10 million raw reads were acquired. In total, 238 unique mature sequences which contain 142 conserved miRNA and 96 novel miRNAs were identified.
2018-12-01 | GSE107802 | GEO