{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Thomas MERCHER"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ATAC-seq"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14204"],"description":["Wild-type (CTRL) and CBFA2T3::GLIS2 induced pluripotent stem cell (iPSC) clones were differentiated into hematopoietic cells in vitro. Cells from day 13 in vitro differentiation were analysed. In addition, cells from CBFA2T3::GLIS2 iPSC were injected into immunodeficient murine recipients that developped leukemia with characteristics of patient leukemia. ATAC-seq was performed to characterize chromatin accessibility in cells from 3 conditions : - Control iPSC-derived hematopoietic cells in vitro (day 13 of differentiation) - CBFA2T3::GLIS2 iPSC-derived hematopoietic cells in vitro (day 13 of differentiation) - CBFA2T3::GLIS2 leukemic cells derived from the engraftment of day 13 CBFA2T3::GLIS2+ iPSC into immunodeficient murine recipients (in vivo)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Librairies were constructed by PCR using the Nextera DNA CD index kit (Illumina) and the NEBNext Ultra II Q5 master mix (NEB).","Nucleic Acid Extraction - PCR purification was performed using Agencourt AMPure XP magnetic beads (Beckman Coulter A63880) in order to remove large fragments and remaining primers. Library quality was assessed using an Agilent 2100 Bioanalyzer using a High Sensitivity DNA chip (Agilent Technologies 5067-4626).","Sample Collection - CD41+ Flow sorted differentiation day-13 hematopoietic cells from ctrl or EG iPSC, leukemic NSG mice or patient samples were collected. 5x104-1x105 GFP+ live-sorted cells were spun at 500g for 5 min, washed with cold DPBS, lysed in cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP40, 3min on ice) and immediately spun at 500g for 10 min. The pelleted nuclei were resuspended in 50 µL of transposase reaction mix (Tagment DNA TDE1 Enzyme and Buffer Kit, Illumina) for 30 min at 39°C.","Sequencing - Libraries were sequenced using Novaseq-6000 sequencer (Illumina) (50bp paired-end reads)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Thomas MERCHER","Elie Robert"],"additional_accession":[]},"is_claimable":false,"name":"Chromatin opening on CBFA2T3::GLIS2 iPSC-derived progenitors","description":"Wild-type (CTRL) and CBFA2T3::GLIS2 induced pluripotent stem cell (iPSC) clones were differentiated into hematopoietic cells in vitro. Cells from day 13 in vitro differentiation were analysed. In addition, cells from CBFA2T3::GLIS2 iPSC were injected into immunodeficient murine recipients that developped leukemia with characteristics of patient leukemia. ATAC-seq was performed to characterize chromatin accessibility in cells from 3 conditions : - Control iPSC-derived hematopoietic cells in vitro (day 13 of differentiation) - CBFA2T3::GLIS2 iPSC-derived hematopoietic cells in vitro (day 13 of differentiation) - CBFA2T3::GLIS2 leukemic cells derived from the engraftment of day 13 CBFA2T3::GLIS2+ iPSC into immunodeficient murine recipients (in vivo).","dates":{"release":"2025-07-09T00:00:00Z","modification":"2025-07-09T16:00:57.051Z","creation":"2024-06-24T22:44:09.239Z"},"accession":"E-MTAB-14204","cross_references":{"ENA":["ERP161399"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0004184"]}}