Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeting individual cells by barcode in pooled sequence libraries

ABSTRACT: Targeting individual cells by barcode in pooled sequence libraries

PROVIDER: PRJNA479863 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Targeting individual cells by barcode in pooled sequence libraries

Project description:Purpose: Selectively sequence desired single cells from pooled single cell libraries

2018-10-15 | GSE116683 | GEO

Targeting individual cells by barcode in pooled sequence libraries.

Project description: Not available

| S-EPMC6326790 | biostudies-literature

Barcode sequencing of Saccharomyces cerevisiae deletion libraries, SYBARIS project

Project description:Barcode sequencing of Saccharomyces cerevisiae deletion libraries, SYBARIS project

| PRJEB1724 | ENA

A Method for High-throughput Production of Sequence-verified DNA Libraries and Strain Collections

Project description:The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. Unfortunately, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI) to address these problems. The method involves integration of a complex library into yeast, site-specific recombination to index (i.e. barcode) library DNA, and then next-generation sequencing to identify clones containing the DNA of interest. We used REDI to generate a molecular probe library (n = ~3,300) that exhibited >96% purity and remarkable uniformity (>95% of probes were within 2-fold relative abundance of the median). Moreover, each sequence-verified probe was readily accessible. We also used REDI to rapidly create an arrayed collection of ~9,000 strains for CRISPR interference in yeast and demonstrate the utility of this collection for highly sensitive phenotypic screening. Our approach will enable a variety of applications requiring accurate, high-quality DNA libraries.

2017-02-14 | GSE81094 | GEO

Single cell RNA-sequencing of T cells to examine barcode swapping

Project description:T cells from OT-I mice were stimulated with 4 different peptide ligands for 6 hours and sorted into two 96-well plates. Cells on each plate were barcoded using a mutually exclusive 8-by-12 set of indexes, such that indexes present on plate 1 were completely absent from plate 2 and vice versa. Libraries from each plate were pooled in equimolar quantities and sequenced on an Illumina HiSeq 4000. Libraries were demultiplexed allowing for all pairs of indexes, including the expected combinations (pairs of barcodes used within each plate) and unexpected combinations (pairs containing one barcode from each plate). This was repeated after sequencing the same pool of libraries on the HiSeq 2500.

2018-06-21 | E-MTAB-6843 | biostudies-arrayexpress

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array based on comparison with the individual samples

Project description:The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. The DNA quantification method, which is important for the homogeneous mixing of DNA in the pooled sample method, has since become fluorescence-based, and additional factors need to be considered including the resolution of batch effects of microarray chips and the heterogeneity of the cellular proportions from which the DNA samples are derived. In this study, four pooled samples were created from 44 individual samples, and EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) were conducted for individual samples and compared with the statistics obtained from the pooled samples.

2023-09-13 | GSE231532 | GEO

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries

Project description:Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. We applied the method in both a cell-centric and gene-centric mode to isolate mRNA fragments from scRNA-seq libraries.

2018-09-04 | GSE119428 | GEO

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries

Project description:Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries

| PRJNA489248 | ENA

HIFI-Barcode-se400

Project description:HIFI-Barcode-se400

| PRJEB29212 | ENA

Human-Mouse Mixture experiment to estimate that contribution of Barcode swapping

Project description:Here we test the impact of barcode swapping in prime-seq. To this end we isolated RNA from human iPSCs and mouse ESCs, processed them separately using prime-seq but pooled them for cDNA amplification.

2022-03-10 | E-MTAB-11456 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data