{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Brian Hendrich"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["ATAC-seq"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15375"],"description":["This study investigates the role of SALL4 in regulating chromatin accessibility. SALL4 was tagged with FKBP to enable dTAG-inducible degradation. ATAC-seq was performed at multiple time-points (1 hour, 4 hours and 8 hours) following dTAG treatment to capture changes in chromatin accessibility upon SALL4 depletion. For each time point, two biological replicates were processed, each with two technical replicates. This dataset aims to characterise the immediate effects of SALL4 loss on chromatin accessibility."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - DNA was extracted using Zymo DNA Clean and Concentrator Kit-5 (Cat. No. D4014).","Library Construction - Barcoding for library prep was performed by PCR amplification using NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs, Cat. No. 10169146) and NEBNext® index primers for Illumina sequencing.","Sample Collection - Cells were cultured on 10cm plates. Cells from all conditions were harvested at the same time using accutase and spun down for 3 min, 600 x g in a swinging bucket rotor at room temperature. Cells were washed in PBS and resuspended in ice-cold NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 5% Glycerol, protease inhibitors) with gentle vortexing. After 10 minutes incubation on ice, the pellet was collected by centrifugation for 4 minutes at 1300 x g at 4C in a swinging bucket rotor. Nuclei was washed with 1X PBS before being resuspended in wash buffer with 10% DMSO to a concentration of 1 million cells per mL. Nuclei was aliquoted in cryotubes and frozen overnight at -80oC in Mr. Frosty containers.","Sequencing - Sequencing was performed on the Illumina NovaSeq X (Flowcell type: 10B).","Growth Protocol - ES cells were cultured on 0.1% gelatin-coated plates in 2i/LIF conditions.","Sample Treatment - For SALL4 depletion, 0.5mM dTAG13 (1:1000 from DMSO stock) was resuspended in pre-warmed culture media and transferred to the cells. 0h dTAG were not treated with dTAG13."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Brian Hendrich","Oluwaseun Ogundele"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-seq data of mouse embryonic stem cells treated with dTAG for SALL4 depletion against untreated control","description":"This study investigates the role of SALL4 in regulating chromatin accessibility. SALL4 was tagged with FKBP to enable dTAG-inducible degradation. ATAC-seq was performed at multiple time-points (1 hour, 4 hours and 8 hours) following dTAG treatment to capture changes in chromatin accessibility upon SALL4 depletion. For each time point, two biological replicates were processed, each with two technical replicates. This dataset aims to characterise the immediate effects of SALL4 loss on chromatin accessibility.","dates":{"release":"2026-01-15T00:00:00Z","modification":"2026-01-15T12:59:29.629Z","creation":"2025-07-21T12:11:14.808Z"},"accession":"E-MTAB-15375","cross_references":{"ENA":["ERP176993"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0004184","EFO_0003969"]}}