Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

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: 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?

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Salmo salar

SUBMITTER: Line Lieblein Røsæg

PROVIDER: E-MTAB-9001 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq of oesophageal adenocarcinoma patient samples

Project description:Open chromatin profiling (ATAC-seq) of human oesophageal adenocarcinoma patient samples.

2020-09-30 | E-MTAB-8447 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma WTSI-OESO_009 (CAM408) organoid treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on WTSI-OESO_009 cells treated with 1000 nM lapatinib for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10306 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma KYAE1 cell line treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on KYAE1 cells treated with 500 nM lapatinib for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10310 | biostudies-arrayexpress

ATAC-seq of human gastric adenocarcinoma NCI-N87 cell line treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on NCI-N87 cells treated with 250nM lapatinib for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10313 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma OE19 cell line treated with lapatinib

Project description:To investigate changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on OE19 cells treated with 500 nM lapatinib for 1, 7 and 35 days and vehicle control (DMSO) for 1 day.

2022-09-26 | E-MTAB-10302 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma ESO26 cell line treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on ESO26 cells treated with 500 nM lapatinib plus 1000 nM MK-2206 (an AKT inhibitor) for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10307 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma OE19 cell line treated with lapatinib for 35 days followed by drug withdrawal

Project description:To investigate whether changes to chromatin accessibility associated with resistance to lapatinib are a stable or a reversible state, we treated OE19 cells with 500 nM lapatinib for 35 days and then withdrew lapatinib for 1, 2, 3 and 14 days. Control cells treated with DMSO for 1 day and 'resistant' cells treated with 500 nM lapatinib for 35 days were also sequenced.

2022-09-26 | E-MTAB-10314 | biostudies-arrayexpress

ATAC-seq of oesophageal adenocarcinoma cell line MFD-1

Project description:The open chromatin of new esophageal adenocarcinoma cell line MFD-1 has been profiled by ATAC-seq.

2018-04-06 | E-MTAB-6720 | biostudies-arrayexpress

Bos taurus ATAC-seq across 88 tissue samples to profile open chromatin regions in the cattle genome

Project description:We performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) using 88 tissue samples to profile open chromatin regions in the cattle genome.

2023-08-24 | E-MTAB-11825 | biostudies-arrayexpress

Timecourse single-cell ATACseq of whole rabbit embryos sampled across gestational days 7, 8 and 9

Project description:We characterised the chromatin accessibility profiles of 34,082 individual cells (post-QC) from whole rabbit embryos spanning gestational days 7, 8 and 9. Cell types were labelled via label transfer of simultaneously generated scRNA-seq of whole rabbit embryos at the same stages. This data was used to determine the chromatin changes occurring during the differentiation of trophoblast to syncytiotrophoblast cells. Cell libraries were prepared using the 10X Genomics Chromium platform.

2022-11-30 | E-MTAB-11804 | 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