Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A cookbook of DNase Hi-C

ABSTRACT: A cookbook of DNase Hi-C

PROVIDER: PRJNA673367 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12951752_1.fastq.gz	Fastqsanger.gz
	SRR12951752_2.fastq.gz	Fastqsanger.gz
	SRR12951753_1.fastq.gz	Fastqsanger.gz
	SRR12951753_2.fastq.gz	Fastqsanger.gz
	SRR12951754_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

A cookbook of DNase Hi-C

Project description:Hi-C technique is widely used to study 3-dimensional chromatin architecture and assemble genomes. Conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in non-uniform genomic coverage. Using sequence-agnostic restriction enzymes such as DNAse I could overcome this limitation. Here we compared different DNAse Hi-C protocols and identified several critical steps which significantly impact protocol efficiency. We proposed a new robust protocol for preparation of DNAse Hi-C libraries, supplemented with experimental controls and computational pipeline for evaluation of libraries quality and data analysis.

2020-10-31 | GSE160484 | GEO

4DNES8R5RDVD - Replicate experiments of DNase Hi-C on RUES2 with DNaseI

Project description:4DNES8R5RDVD - Replicate experiments of DNase Hi-C on RUES2 with DNaseI

| PRJNA919044 | ENA

A cookbook for DNase Hi-C.

Project description:BackgroundThe Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation.ResultsIn this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming.ConclusionsWe propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

| S-EPMC7981840 | biostudies-literature

4DNESX5HHBRP - Replicate experiments of DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI

Project description:4DNESX5HHBRP - Replicate experiments of DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI

| PRJNA919047 | ENA

intact Hi-C from placenta (ENCSR395DZW)

Project description:human placenta intact hi-c dnase For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2023-07-24 | GSE237343 | GEO

intact Hi-C from ovary (ENCSR782YIX)

Project description:w73 ovary intact dnase hi-c For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2023-07-24 | GSE238023 | GEO

4DNES2D4WOKP - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial cell with DNaseI

Project description:4DNES2D4WOKP - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial cell with DNaseI

| PRJNA919041 | ENA

SMARCA4 Rescue Profiling [Dnase]

Project description:SMARCA4 Rescue Profiling [Dnase]

| PRJNA547550 | ENA

4DNES6MT2D6K - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI

Project description:4DNES6MT2D6K - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI

| PRJNA919045 | ENA

Zebrafish Globin Locus (DNAse)

Project description:Genome-wide analysis of H3K4me3 modifications, Gata1 binding, and DNase I hypersensitivity sites in zebrafish adult red blood cells Zebrafish peripheral blood nuclei were isolated for DNase I hypersensitivity assays. Total DNA were purified using the Proteinase K digestion and Phenol-Chloroform extraction. Small DNase I fragments from the DNaseI treatement were enriched using a sucrose gradient. These ends were then labeled and amplified during library construction and for Solexa sequencing

2012-02-17 | E-GEOD-35875 | biostudies-arrayexpress

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