Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Equine FAANG ATAC-seq Pilot

ABSTRACT: Equine FAANG ATAC-seq Pilot

PROVIDER: PRJEB41317 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR4835470_1.fastq.gz	Fastqsanger.gz
	ERR4835470_2.fastq.gz	Fastqsanger.gz
	ERR4835461_1.fastq.gz	Fastqsanger.gz
	ERR4835461_2.fastq.gz	Fastqsanger.gz
	ERR4835471_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

equine FAANG CTCF

Project description:CTCF ChIP-seq for equine FAANG project

| PRJEB41079 | ENA

Open Chromatin Annotations in Eight Prioritized Equine FAANG Tissues

Project description:ATAC-seq of Eight Prioritized Equine FAANG Tissues

| PRJEB53037 | ENA

AQUA-FAANG ATAC-seq for Cyprinus carpio head kidney tissues

Project description: Not available

| S-BSST1279 | biostudies-other

Successful ATAC-Seq From Snap-Frozen Equine Tissues.

Project description:An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000-33,000 accessible chromatin regions in lamina and 22-61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments.

| S-EPMC8242358 | biostudies-literature

Geuvadis RNA-seq five individual pilot

Project description:Pilot RNA-seq dataset created by the Geuvadis consortium (www.geuvadis.org)

2010-04-14 | E-GEUV-4 | biostudies-arrayexpress

FAANG Pig IPECJ2 cell line

Project description:FAANG Pig IPECJ2 cell line

| PRJEB59474 | ENA

WUR-FAANG

Project description:Wageningen University & Research Animal Breeding and Genomics FAANG data from three boars.

| PRJEB19268 | ENA

Bulk ATAC-seq of primate cerebral organoids

Project description:Bulk ATAC-seq was performed on human, chimpanzee, bonobo, and macaque stem cell-derived cerebral organoids. ATAC-seq was performed on day 60 (2 months old) and day 120 (4 months old) cerebral organoids.

2019-10-16 | E-MTAB-8228 | biostudies-arrayexpress

Chordoma ATAC-Seq

Project description:Chromatin profiling of chordoma collected by the Broad chordoma target discovery project paired end ATAC-Seq profiling in the UCH2 and MUGCHOR chordoma cell lines

2015-07-11 | E-GEOD-70771 | biostudies-arrayexpress

Equine Laminitis vs Control.

Project description:Equine lameller tissues were collected to compare normal vs laminitis generated differences in transcriptom level. Keywords: Laminitis, Equine, Diseased foot

2008-03-22 | GSE7360 | 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