NextSeq 500 paired end sequencing; ATAC-seq in neuroblastoma IMR-32 cell line
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Neural
Cell type
IMR-32
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma
Attributes by original data submitter
Sample
ENA first public
2018-08-16
ENA last update
2018-03-02
ENA-CHECKLIST
ERC000011
External Id
SAMEA104664386
INSDC center alias
Center for Medical Genetics, Gent, Belgium Cancer Research Institute Gent, Belgium
INSDC center name
Center for Medical Genetics, Gent, Belgium Cancer Research Institute Gent, Belgium
INSDC first public
2018-08-16T17:02:55Z
INSDC last update
2018-03-02T15:53:14Z
INSDC status
public
Submitter Id
E-MTAB-6562:Sample 1
broker name
ArrayExpress
cell line
IMR-32
cell type
neuroblast
common name
human
disease
neuroblastoma
metastatic site
abdominal mass
organism part
brain
sample name
E-MTAB-6562:Sample 1
Sequenced DNA Library
library_name
Sample 1_p
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
PCR
library_construction_protocol
50,000 cells were harvested and spin down for 5 min at 800g. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37°C in a 5% CO2 humid atmosphere ATAC-seq was performed as previously described with minor changes ( doi: 10.1002/0471142727.mb2129s109, Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Illumina). Samples were purified using the MinElute kit (Qiagen) The transposased DNA fragments were amplified and purified using Agencourt AMPure XP beads (Beckmamn Coulter). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat.no. KK4854)