ATAC_HEKdBcat_LGK_rep2
Homo sapiens
Protocols: Cells were harvested by incubation in Trypsin EDTA 0.25% (25-200-056, Thermo Fisher Scientific) and washed with PBS. Cells were cultured in DMEM (41966-029, Gibco – Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (12133C, Sigma-Aldrich) and 10 U/ml Penicillin-Streptomycin (15276355, Gibco - Thermo Fisher Scientific). Cells were passaged by incubation in Trypsin EDTA 0.25% (25-200-056, Thermo Fisher Scientific).  ΔCTNNB1 HEK293T cells were pre-treated with the PORCN inhibitor LGK974 (10 nM) for 24 hours, followed by stimulation with the GSK3 inhibitor CHIR99021 (10 µM) for 4 hours to activate Wnt/β-catenin signaling. Adapter trimming and quality filtering were performed using bbduk from the BBTools suite (v39.01) in paired-end mode. Adapter removal used the parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo, and low-quality bases were trimmed using qtrim=l trimq=30, removing reads with Phred scores < 30.  n = 3 samples,  with 5x104 cells per sample were processed for ATAC-seq according to previously published protocols (Buenrostro et al., 2015). Briefly, cells were washed with cold PBS, nuclear extracted in ice cold lysis buffer (Tris-HCl pH 7.4 [10 mM], NaCl [10 mM], MgCl2 [3 mM], IGEPAL CA-630 [0.1%]), and pelleted. Pelleted nuclei were incubated in 50 μL transposition reaction mix (20034210, Illumina) at 370C for 30 minutes and the tagmented DNA was purified using QUAGEN Minielute PCR purification.  For Library preparation, transposed DNA fragments were amplified for 13 cycles in the presence of Custom Nextera PCR primers (Buenrostro et al., 2013) using the NEBNext High-Fidelity 2x PCR Master Mix (Cat. #M0541, New England Biolabs). Libraries were purified using the High Pure PCR Production Purification Kit (11732676001, Roche/ Sigma-Aldrich). Libraries were validated on an Agilent 2100 and quantified using qPCR.
ENA first public
2026-05-24
INSDC center name
Linköping University
INSDC status
public
Submitter Id
E-MTAB-16975:ATAC_HEKdBcat_LGK_rep2
broker name
ArrayExpress
cell line
HEK293T
cell type
embryonic kidney cell untreated
collection date
not collected
common name
human
developmental stage
embryo stage
disease
normal
genotype
CTNNB1 knock-out
geographic location (country and/or sea)
not collected
isolate
not applicable
organism part
kidney
replicate
2
sample name
E-MTAB-16975:ATAC_HEKdBcat_LGK_rep2
scientific_name
Homo sapiens