Illumina HiSeq 4000 paired end sequencing; ATAC-seq of Het1A cells with overexpression of HNF4A or GATA6
ATAC-seq of Het1A cells with overexpression of HNF4A or GATA6
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.
Experimental Factor: phenotype
doxycyclin mediated overexpression of HNF4A
Experimental Factor: time
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