{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Isaura Frost"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15741"],"description":["This experiment investigates how different intracellular delivery methods, specifically filtroporation (FP) and electroporation (EP) affect gene editing efficiency and cellular responses in human hematopoietic stem and progenitor cells. By comparing these methods, results show how mechanical versus electrical membrane disruption influences gene expression, cell fate, and membrane repair mechanisms. This study also explores the molecular processes involved in rapid membrane repair, highlighting the roles of calcium signaling and key repair proteins such as GRAF1, SNAP23, and CHMP4B."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted and purified from HSPCs after cell lysis (~400,000 cells per condition in triplicates) using a Qiagen RNeasy Mini Kit.","Sample Collection - Wild type and KO Jurkat cells (American Type Culture Collection, Inc., ATCC) were cultured in 1× Roswell Park Memorial Institute Medium (RPMI) 1640.","Sequencing - Samples were sequenced on a NovaSeq S1 2x50 with a read depth of 35 M reads/sample.","Library Construction - RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads following the manufacturer’s protocol which included reverse transcription of mRNA, ligation of adaptors, and PCR enrichment of libraries. Libary pool was 10nM."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore! (Parameter - Quality limit: Phred 20). Trimmed sequence reads were mapped to GrCh38 using STAR (Parameters - mismatch cost: 2, insertion cost: 2, deletion cost: 2, length fraction: 0.7, similarity fraction: 0.7) and Salmon (Parameters - mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.65, similarity fraction: 0.65).","Data Transformation - Read count extraction and normalization were all performed using default software in DESeq2."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Qiagen RNeasy Mini Kit","R","Illumina NovaSeq 6000","NEBNext Ultra II Directional RNA Library Prep","Linux Bash Scripting","With L-glutamine supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (10,000 units/mL penicillin and 10 mg/mL streptomycin) (Gibco)."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Membrane Repair Following Filtroporation-Induced Cell Permeabilization"],"pubmed_authors":["Isaura M. Frost, Ruby Sims, Anya Yakimenko, Rachel Ma, Maximilian Floridia, Ruth A. Foley, Emily Duggan, Kelly Y. Cai, Kelsey Jorgensen, Emily Skuratovsky, Paul S. Weiss,  Steven J. Jonas","Isaura Frost"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of human hematopoietic stem and progenitor cells to study membrane repair following electroporation (EP) or filtroporation (FP) disruption based strategies for intracellular delivery","description":"This experiment investigates how different intracellular delivery methods, specifically filtroporation (FP) and electroporation (EP) affect gene editing efficiency and cellular responses in human hematopoietic stem and progenitor cells. By comparing these methods, results show how mechanical versus electrical membrane disruption influences gene expression, cell fate, and membrane repair mechanisms. This study also explores the molecular processes involved in rapid membrane repair, highlighting the roles of calcium signaling and key repair proteins such as GRAF1, SNAP23, and CHMP4B.","dates":{"release":"2025-10-30T00:00:00Z","modification":"2026-05-31T01:45:18.33Z","creation":"2025-10-15T14:56:50.429Z"},"accession":"E-MTAB-15741","cross_references":{"ENA":["ERP182245"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}