Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [3pDGE]

ABSTRACT: Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [3pDGE]

PROVIDER: PRJNA486816 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7723360_1.fastq.gz	Fastqsanger.gz
	SRR7723360_2.fastq.gz	Fastqsanger.gz
	SRR7723370_1.fastq.gz	Fastqsanger.gz
	SRR7723370_2.fastq.gz	Fastqsanger.gz
	SRR7723380_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 190

Similar Datasets

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [microarray]

Project description:Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [microarray]

| PRJNA486814 | ENA

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [SFL]

Project description:Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [SFL]

| PRJNA486817 | ENA

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [microarray]

Project description:In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3’ digital gene expression (3’ DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3’ DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.

2019-03-28 | GSE118799 | GEO

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [3pDGE]

2019-03-28 | GSE118798 | GEO

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [SFL]

2019-03-28 | GSE118797 | GEO

Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques.

Project description:The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine multiple samples into a single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq, microarrays, as well as another low-cost highly multiplexed technique known as 3' digital gene expression (3'DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3'DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.

| S-EPMC6411637 | biostudies-literature

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

Project description:High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting. Comparison of ChIP-seq libraries constructed from 100 pg DNA (this study) and nanograms of DNA (modENCODE). ChIP antibody: H3K27me3, Active Motif 31955.

2013-07-01 | E-GEOD-48431 | biostudies-arrayexpress

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

2013-07-01 | GSE48431 | GEO

Highly multiplexed single-cell quantitative PCR

Project description:Highly multiplexed single-cell quantitative PCR

| PRJNA398516 | ENA

Highly multiplexed spatial transcriptomics in bacteria

Project description:Highly multiplexed spatial transcriptomics in bacteria

| PRJNA1117432 | ENA