Illumina HiSeq 4000 paired end sequencing; ATAC-seq of Het1A cells with overexpression of HNF4A or GATA6
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Cardiovascular
Cell type
Het-1A
Primary Tissue
Esophagus
Tissue Diagnosis
Normal
Attributes by original data submitter
Sample
ENA first public
2018-08-30
ENA last update
2018-06-22
ENA-CHECKLIST
ERC000011
External Id
SAMEA4753714
INSDC center alias
UOM
INSDC center name
University of Manchester
INSDC first public
2018-08-30T17:02:49Z
INSDC last update
2018-06-22T14:00:08Z
INSDC status
public
Submitter Id
E-MTAB-6931:Het1A-HNF4A_2d_rep2
broker name
ArrayExpress
cell line
Het1A
cell type
epithelial cell
common name
human
disease
normal
genotype
HNF4A-tet-on
organism part
esophagus
phenotype
doxycyclin mediated overexpression of HNF4A
sample name
E-MTAB-6931:Het1A-HNF4A_2d_rep2
Sequenced DNA Library
library_name
Het1A-HNF4A_2d_rep2_p
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
The cells were generated by infecting cells with 2nd generation lentiviruses. The genes are under Tet-on control. 2d and 4d indicates either doxycycline induction for 2 or 4 days. Het1A, Het1A-HNF4A and Het1A-GATA6 cells were cultured in DMEM (+10% FBS and 1% PenStrep) with 100ng/mL doxycycline for 2 or 4 days. Cells were trypsinised and counted. 50000 cells were taken forward for Tn5 reaction. 50000 cells were lysed in ATAC lysis buffer and Tn5 reactions were performed as described in Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba, Howard Y. Chang and William J. Greenleaf. doi:10.1038/nmeth.2688 Libraries were constructed by amplifying transposed DNA with Illumina Nextera adapters.