Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-amplified Barcodes on Slides for Spatial Transcriptomics Sequencing

ABSTRACT: Using microfluidics, well-defined barcodes were generated on the slide surface by cross-amplification, followed by high-throughput sequencing using Novaseq to detect spatial transcriptomic information in the mouse brain.

ORGANISM(S): Mus musculus

PROVIDER: GSE211858 | GEO | 2022/08/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Arthropod COI barcodes amplified from Purple Martin fecal samples

Project description:Arthropod COI barcodes amplified from Purple Martin fecal samples Targeted loci environmental

| PRJNA688294 | ENA

Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes

Project description:RNA-Seq is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends. After PCR, we applied paired-end deep sequencing to read the two barcodes and cDNA sequences. Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence. We optimized the barcodes to be unambiguously identifiable even in the presence of multiple sequencing errors. This method allows counting with single copy resolution despite sequence-dependent bias and PCR amplification noise, and is analogous to digital PCR but amendable to quantifying a whole transcriptome. We demonstrated transcriptome profiling of E. coli with more accurate and reproducible quantification than conventional RNA-Seq.

2012-01-07 | GSE34449 | GEO

RNA-Seq of STAR-PROM Barcodes

Project description:We report the application of a massively parallel STAR-PROM assay based on the RNA-seq of 3000+ luciferase barcodes

2017-01-12 | GSE81271 | GEO

Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes

2012-01-07 | E-GEOD-34449 | biostudies-arrayexpress

RNA Encoded Peptide Barcodes Enable Efficient in vivo Screening of RNA Delivery Systems

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

RABID barcodes from naive astrocyte networks

Project description:RABID barcodes from naive astrocyte networks

| PRJNA658374 | ENA

Digital counting of nucleic acid molecules using random base molecular barcodes

Project description:Several template DNA molecules with random base molecular barcodes were amplified and sequenced, and the efficacy of the random base barcode for digital counting was shown.

2017-10-19 | GSE94895 | GEO

Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp

Project description:Most single cell RNA sequencing protocols start with single cells dispersed from intact tissue. High-throughput processing of the separated cells is enabled using microfluidics platforms. However, dissociation of tissue results in loss of information about cell location and morphology and potentially alters the transcriptome. An alternative approach for collecting RNA from single cells is to re-purpose the electrophysiological technique of patch clamp recording. A hollow patch pipette is attached to individual cells, enabling the recording of electrical activity, after which the cytoplasm may be extracted for single cell RNA-Seq (“Patch-Seq”). Since the tissue is not disaggregated, the location of cells is readily determined, and the morphology of the cells is maintained, making possible the correlation of single cell transcriptomes with cell location, morphology and electrophysiology. Recent Patch-Seq studies utilizes PCR amplification to increase amount of nucleic acid material to the level required for current sequencing technologies. PCR is prone to create biased libraries – especially with the extremely high degrees of exponential amplification required for single cell amounts of RNA. We compared a PCR-based approach with linear amplifications and demonstrate that aRNA amplification (in vitro transcription, IVT) is more sensitive and robust for single cell RNA collected by a patch clamp pipette.

2020-01-25 | GSE144216 | GEO

RABID barcodes from priming EAE astrocyte networks

Project description:RABID barcodes from priming EAE astrocyte networks

| PRJNA694051 | ENA

RABID barcodes from peak EAE astrocyte networks

Project description:RABID barcodes from peak EAE astrocyte networks

| PRJNA658556 | ENA