Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DT4DDS - Characterization of Errors and Biases in DNA Data Storage

ABSTRACT: DT4DDS - Characterization of Errors and Biases in DNA Data Storage

PROVIDER: PRJEB65931 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR12033900_1.fastq.gz	Fastqsanger.gz
	ERR12033900_2.fastq.gz	Fastqsanger.gz
	ERR12033901_1.fastq.gz	Fastqsanger.gz
	ERR12033901_2.fastq.gz	Fastqsanger.gz
	ERR12033902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 322

Similar Datasets

A digital twin for DNA data storage based on comprehensive quantification of errors and biases.

Project description:Archiving data in synthetic DNA offers unprecedented storage density and longevity. Handling and storage introduce errors and biases into DNA-based storage systems, necessitating the use of Error Correction Coding (ECC) which comes at the cost of added redundancy. However, insufficient data on these errors and biases, as well as a lack of modeling tools, limit data-driven ECC development and experimental design. In this study, we present a comprehensive characterisation of the error sources and biases present in the most common DNA data storage workflows, including commercial DNA synthesis, PCR, decay by accelerated aging, and sequencing-by-synthesis. Using the data from 40 sequencing experiments, we build a digital twin of the DNA data storage process, capable of simulating state-of-the-art workflows and reproducing their experimental results. We showcase the digital twin's ability to replace experiments and rationalize the design of redundancy in two case studies, highlighting opportunities for tangible cost savings and data-driven ECC development.

| S-EPMC10533828 | biostudies-literature

Davos DNA data storage

Project description:Davos DNA data storage challenge / Bitcoin challenge

| PRJEB41462 | ENA

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq]

Project description:Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes sequences? that are critical for the removal of PCR amplification biases within both bulk and single-cell sequencing experiments. However, the impact that PCR and sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We demonstrate that PCR errors and not sequencing errors are the main source of inaccuracy in sequencing data and that the use of UMIs synthesized with homotrimeric nucleoside building blocks provides a solution to pinpoint and remove errors, allowing absolute counting of sequenced molecules.

2023-06-01 | GSE218901 | GEO

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [RNA-seq]

2023-06-01 | GSE218899 | GEO

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

Project description:Background: Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods. What has been lacking is a systematic comparison of their relative biases and benefits. Results: Here, we compare gene expression and cellular composition of single cell suspensions prepared from adult mouse kidney using two tissue dissociation protocols. For each sample we also compare fresh cells to cryopreserved and methanol-fixed cells. Lastly, we compare this single-cell data to that generated using three single-nucleus RNA sequencing workflows. Our data confirms prior reports that digestion on ice avoids the stress response observed with 37°C dissociation. It also reveals cell types more abundant either in the cold or warm dissociations that may represent populations that require gentler or harsher conditions to be released intact. For cell storage, cryopreservation of dissociated cells results in a major loss of epithelial cell types; in contrast, methanol fixation maintains the cellular composition but suffers from ambient RNA leakage. Finally, cell type composition differences are observed between single-cell and single-nucleus RNA sequencing libraries. In particular, we note an under-representation of T, B and NK lymphocytes in the single-nucleus libraries. Conclusions: Systematic comparison of recovered cell types and their transcriptional profiles across the workflows has highlighted protocol-specific biases and thus enables researchers starting single cell experiments to make an informed choice.

2020-05-11 | GSE141115 | GEO

Codec benchmarking for DNA data storage

Project description:Codec benchmarking for DNA data storage

| PRJEB90546 | ENA

Efficient DNA based data storage using shortmer combinatorial encoding

Project description:Combinatorial DNA storage

| PRJEB71104 | ENA

composite DNA storage

Project description:DNA storage of digital media using composite DNA

| PRJEB32427 | ENA

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

Project description:Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows