{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Xing Wang"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13512"],"description":["AML cell line Kasumi-1 was treated with aptamers targeting cell surface proteins CD117 and CD123. The samples were collected for RNA Sequencing 12 and 24 hours post treatment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted using Trizol following manufacturers protocol.","Sequencing - Sequencing was performed using Illumina NovaSeq system 100 bp single reads.","Growth Protocol - Cells were grown in HPLM media supplemented with 10% fetal bovine serum with antibiotic-antimycotic solution.","Sample Collection - Cells were collected by centrifugation post experimental time points and stored and shipped at -80 C  to the sequencing facility.","Sample Treatment - Aptamers were stored in 10 mM HEPES buffer (pH 7.2) containing 100 mM NaCl and 12 mM MgCl2 and cells were incubated in the same buffer during the treatment period of 6 h.","Library Construction - Sequencing library was constructing using polyA enrichment PCR."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Salmon version 1.5.2 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. Gene-level counts were then estimated based on transcript-level counts using the “lengthScaledTPM” method from the tximport package.","Data Transformation - The TMM (trimmed mean of M values) normalization in the edgeR package was used for data normalization and filtering."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["ThermoScientific, IDT","Illumina NovaSeq 6000","Applied Biosystems","ThermoScientific","ThermoScientific, VWR","Robotics"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Abhisek Dwivedy","Xing Wang"],"additional_accession":[]},"is_claimable":false,"name":"Effect of aptamer treatment on AML cells","description":"AML cell line Kasumi-1 was treated with aptamers targeting cell surface proteins CD117 and CD123. The samples were collected for RNA Sequencing 12 and 24 hours post treatment.","dates":{"release":"2025-06-30T00:00:00Z","modification":"2024-11-03T15:00:16.781Z","creation":"2023-11-01T20:59:51.328Z"},"accession":"E-MTAB-13512","cross_references":{"ENA":["ERP153083"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}