biostudies-arrayexpressTamina WeissHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16975Wnt/β-catenin signaling is generally thought to activate transcription primarily through pre-accessible regulatory elements. However, we previously identified cases in which β-catenin associates with initially inaccessible chromatin regions that subsequently gain accessibility (E-MTAB-12076, Pagella et. al., (2023) Cell Systems). To determine whether stimulus-dependent chromatin opening requires β-catenin, we performed ATAC-seq in β-catenin knockout (ΔCTNNB1) human embryonic kidney 293T (HEK293T) cells, both prior to and 4 hours following pathway activation.biostudies-arrayexpressSample Collection - Cells were harvested by incubation in Trypsin EDTA 0.25% (25-200-056, Thermo Fisher Scientific) and washed with PBS.Sequencing - Libraries were sequenced on the Illumina NovaSeq 6000 S4 flowcell with PE150 according to results from library quality control and expected data volume.Nucleic Acid Extraction - 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.Sample Treatment - 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.Growth Protocol - 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).Library Construction - 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - For visualization, replicates were merged using SAMTools (v1.22) merge and genome-wide coverage tracks as BigWig format were generated using DeepTools’s (v.3.5.6) bamCoverage with CPM normalization and -bin10 --extendReads --centerReads --ignoreDublicates.Sequence Alignment - Reads were aligned to the GRCh38 reference genome using Bowtie2 (v2.4.5; (Langmead and Salzberg, 2012)) in paired-end mode with the --very-sensitive-local setting. Resulting SAM files were converted to BAM format, sorted by genomic coordinates, and indexed using Samtools (v1.22; (Danecek et al., 2021)).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000ATAC-seqHomo sapiensClaudio CantùPierfrancesco PagellaTamina WeissfalseATAC-seq time-course profiling upon Wnt stimulation in ΔCTNNB1 HEK293T cellsWnt/β-catenin signaling is generally thought to activate transcription primarily through pre-accessible regulatory elements. However, we previously identified cases in which β-catenin associates with initially inaccessible chromatin regions that subsequently gain accessibility (E-MTAB-12076, Pagella et. al., (2023) Cell Systems). To determine whether stimulus-dependent chromatin opening requires β-catenin, we performed ATAC-seq in β-catenin knockout (ΔCTNNB1) human embryonic kidney 293T (HEK293T) cells, both prior to and 4 hours following pathway activation.2026-05-24T00:00:00Z2026-05-26T20:15:27.212Z2026-04-29T13:47:58.187ZE-MTAB-16975ERP192778E-MTAB-12076EFO_0002944EFO_0007045EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969