Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MOWChIP-seq for low-input and high-throughput profiling of genome-wide histone modifications

ABSTRACT: MOWChIP-seq for low-input and high-throughput profiling of genome-wide histone modifications

PROVIDER: PRJNA509365 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8311110.fastq.gz	Fastqsanger.gz
	SRR8311111.fastq.gz	Fastqsanger.gz
	SRR8311112.fastq.gz	Fastqsanger.gz
	SRR8311113.fastq.gz	Fastqsanger.gz
	SRR8311109.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

MOWChIP-seq for low-input and high-throughput profiling of genome-wide histone modifications

Project description:Epigenetic mechanisms such as histone modifications and DNA methylation form a critical layer of control that regulates gene activities. Histone modifications play critical roles in adaptive tuning of chromatin structures. Profiling various histone modifications at the genome scale using primary tissues from animal and human samples is an important step for functional studies of epigenomes and epigenomics-based precision medicine. Because the profile of a histone mark is highly specific to a particular cell type, isolation of a cell type of interest from primary tissues is often necessary to generate a homogeneous cell population and such operation tends to yield a low number of cells. In addition, high-throughput processing is desired in such effort due to the number of histone marks of interests and the potential volume of samples in a hospital setting. In this protocol, we describe detailed information on device fabrication, setup, and operation of microfluidic oscillatory washing-based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq) for profiling histone modifications using as few as 30-100 cells per assay with a throughput as high as 8 assays in a run. The critical step of MOWChIP-seq operation involves flowing of chromatin fragments through a packed bed of antibody-coated beads followed by a vigorous microfluidic oscillatory washing. The ChIP process is semi-automated for reduced labor and improved reproducibility. We have used the protocol to study a number of histone modifications in various types of mouse and human tissue types ranging from isolated nuclei of brain cells to cell subtypes isolated from human breast tissues.

2019-08-31 | GSE123606 | GEO

Microfluidic low-input fluidized-bed enabled ChIP-seq device for automated and parallel analysis of histone modifications

Project description:Genome-wide epigenetic changes such as histone modifications form a critical layer of gene regulations and have been implicated in a number of different disorders such as cancer and inflammation. Progress has made to decrease the input required for gold-standard genome-wide profiling tools like chromatin immunoprecipitation followed by next generation sequencing (i.e. ChIP-seq) to allow scarce primary tissues of specific type from patients and lab animals to be tested. However, there has been very little effort to rapidly increase the throughput of these low-input tools. In this report, we demonstrate LIFE-ChIP-seq (Low-Input Fluidized-bed Enabled Chromatin Immunoprecipitation combined with sequencing), an automated and high-throughput microfluidic platform capable of running multiple sets of ChIP assays in as little as 1 h with as few as 50 cells per assay. Our technology will enable testing of a large number of samples and replicates with low-abundance primary samples in the context of precision medicine.

2018-06-01 | GSE102932 | GEO

CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP]

Project description:we develop a robut low input cell and high throughput single cell ChIP method used for both native and fixed in vitro cultured cells and intact tissue

2019-07-15 | GSE129333 | GEO

CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP]

Project description:CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP]

| PRJNA531012 | ENA

Chromatin integration labeling for mapping multiple DNA binding proteins and modifications with low input.

Project description:Chromatin integration labeling for mapping multiple DNA binding proteins and modifications with low input.

| PRJNA590476 | ENA

Low-input Hi-C library construction

Project description:Low-input Hi-C library construction

| PRJNA975160 | ENA

Low input RNA-seq of HSCs.

Project description:Low input RNA-seq of HSCs.

| PRJNA834789 | ENA

Fast Low-Input Efficient Hi-C

Project description:Fast Low-Input Efficient Hi-C

| PRJNA1157835 | ENA

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

Project description:Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

| PRJNA271674 | ENA

High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing

Project description:We developed a high-throughput sequencing protocol that efficiently captures small RNAs from low input samples while minimizing inherent biases associated with library production. The protocol was builds on previously published method that adds a barcode to samples at the earliest step in preparation such that all downstream manipulations can be performed on a pool of many samples thereby greatly reducing reagent usage and workload. We optimized adapter concentrations and showed modified adapters greatly increases the efficiency of small RNA capture. This work also demonstrates that unique molecular identifiers incorporated into the adapters can be used to bioinformatically remove PCR duplication.

2019-01-31 | GSE109162 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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