Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fresh versus slow-frozen ATACseq samples for salmon tissues

ABSTRACT: Fresh versus slow-frozen ATACseq samples for salmon tissues

PROVIDER: PRJEB38052 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR4078170_1.fastq.gz	Fastqsanger.gz
	ERR4078170_2.fastq.gz	Fastqsanger.gz
	ERR4078180_1.fastq.gz	Fastqsanger.gz
	ERR4078180_2.fastq.gz	Fastqsanger.gz
	ERR4078190_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 320

Similar Datasets

Fresh versus slow-frozen ATACseq samples for salmon tissues

Project description:When sampling many samples at locations with poor laboratory facilities, the ability of freezing samples for later processising is crucial. ATAC-seq on fresh tissue is still considered the star method. Freezing has shown to affect chromatin architecture and nucleosome pattern. However, the freezing method might determine the chromatin integrity. We therefore ask whether or not slow frozen samples give the same results as fresh samples when assaying tissues for transposase accessible chromatin?

2020-05-08 | E-MTAB-9001 | biostudies-arrayexpress

Fresh/Frozen Project

Project description:The Ocular Surface Microbiome: A Comparison of Fresh and Frozen Samples

| PRJEB60099 | ENA

Fresh/Frozen Project

Project description:The Ocular Surface Microbiome: A Comparison of Fresh and Frozen Samples

| PRJEB60101 | ENA

miRNA experiment of fresh frozen colonic biopsy samples

Project description:The aim of the present study was to perform an additional global miRNA microarray analysis of tubular and tubulovillous adenoma biopsy specimen completed with colorectal adenocarcinomas using fresh frozen tisse

2016-10-19 | GSE83924 | GEO

Whole genome bisulfite sequencing and Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis (WGBS)

Project description:We compared the global DNA methylation levels of hairless mouse epidermis using the Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulfite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of xxx,xxx CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.996) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.

2022-09-23 | GSE213747 | GEO

Single Cell RNA Sequencing of Fresh and Frozen Human Atheroma Tissue

Project description:We conducted a comparison of scRNA-seq on four paired fresh and cryopreserved atheroma samples, two from coronary arteries and two from carotid arteries, to determine whether it is possible to obtain comparable data from frozen samples. After enzymatic digestion into single cell suspensions, we sorted CD45+ cells from half of each sample and immediately processed these using the 10X Genomics scRNA-seq workflow after collection, while the other half was frozen in liquid nitrogen. After cryopreservation for an average of 7 days, the other half of each sample was thawed and sorted identically to the fresh samples.

2022-10-31 | GSE179159 | GEO

Comparison of fresh and slow-frozen cancer samples for different applications

Project description:Surplus tissues from multiple solid human cancers directly slow-frozen after resection can subsequently be used for different types of methods including the establishment of 2D, 3D, and ex vivo cultures as well as single cell RNA sequencing (scRNAseq) with similar results when compared to freshly analyzed material.

| EGAS00001005891 | EGA

Comparison of FFPE and fresh frozen prostate tissues using PCT SWATH

Project description:We compared the proteomes of FFPE and fresh frozen tissues (both tumorous and non-tumorous) from 16 prostate cancer patients using pressure cycling technology and SWATH-MS.

2019-10-07 | PXD004691 | Pride

Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

Project description:We compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory

2022-09-23 | GSE213717 | GEO

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using one-colour Agilent microarrays

Project description:Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

2015-10-14 | GSE62842 | 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