Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Performance of a highly scalable and extraction-free RNA-seq method

ABSTRACT: Performance of a highly scalable and extraction-free RNA-seq method

PROVIDER: PRJNA691505 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13416023.fastq.gz	Fastqsanger.gz
	SRR13416024.fastq.gz	Fastqsanger.gz
	SRR13416025.fastq.gz	Fastqsanger.gz
	SRR13416026.fastq.gz	Fastqsanger.gz
	SRR13416027.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 108

Similar Datasets

Performance of a highly scalable and extraction-free RNA-seq method

Project description:RNA-seq workflows have become progressively more efficient over time however, RNA extraction still remains a significant bottleneck. For small numbers of sample, highly efficient RNA extraction is simple to perform but becomes costly and laborious at the scale of hundreds of samples. Our prior work has demonstrated that qPCR can be accurately performed using bulk cells samples lysate instead of RNA extraction. We combined this method with the recently developed simple method for rapid RNA-seq library prep; Smart-3SEQ (Foley et al., 2019) and hypothesized that bulk RNA-seq can be performed in a multi-well plate format, and at low cost by performing RNA-seq library prep cDNA synthesis using in-lysate RNA followed by Smart-3SEQ. The result shows success of our approach in various levels: 1) all quality control measures were achieved, 2) Gene expression profiles, gene differential expression and the response patterns reported by in-lysate and purified RNA library highly correlate with each other, and 3) in-lysate RNA-seq library prep performed similar to the gold standard used here (Illumina Truseq) for DEG calling.

2021-01-22 | GSE164650 | GEO

DNA extraction method from alfalfa

Project description:DNA extraction method from alfalfa Metagenome

| PRJNA901244 | ENA

Method DNA extraction Mars simulant soil

Project description:DNA extraction method for synthetic Mars soil

| PRJEB68335 | ENA

A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells

Project description:A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells

| PRJNA603321 | ENA

Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients

Project description:Genome-wide analysis of cell-free DNA (cfDNA) methylation profile has been recognized as a promising approach for sensitive and specific detection of many cancers. However, scaling such genome-wide assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We have shown that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation with high sensitivity and quantitative tracking of colorectal cancer patient’s response to treatment, at much reduced sequencing cost suitable for frequent monitoring. We also show, for the first time, tumor epigenetic subtyping from cfDNA using Heatrich-BS, which could enable patient stratification from non-invasive liquid biopsy. As such, Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.

2022-05-13 | GSE202606 | GEO

DNA Extraction

Project description:DNA extraction method targeted loci environmental

| PRJNA315949 | ENA

Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients [CRC]

2022-07-21 | GSE208596 | GEO

Highly scalable generation of DNA methylation profiles in single cells

Project description:We present a novel method: single-cell combinatorial indexing for methylation analysis (sci-MET), which is the first highly scalable assay for whole genome methylation profiling of single cells. We use sci-MET to produce 3,282 total single-cell bisulfite sequencing libraries and achieve read alignment rates of 68± 8%, comparable to those of bulk cell methods. As a proof of concept, we applied sci-MET to deconvolve the cellular identity of a mixture of three human cell lines. Next, we applied sci-MET to mouse cortical tissue, which successfully identified excitatory and inhibitory neuronal populations as well as non-neuronal cell types.

2018-04-12 | GSE112554 | GEO

A modified isooctane-based DNA extraction method from crude oil

Project description:Isooctane-based DNA extraction method from crude oil

| PRJEB65234 | ENA

A multiparametric extraction method for the molecular characterization of Vn96-isolated plasma extracellular vesicles

Project description:We demonstrate a method for the DNA, RNA and Protein extraction of plasma extracellular vesicles.

2020-01-08 | GSE133991 | GEO