{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Rebecca Hannah"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16782"],"description":["As a rapid Stem11 scoring platform, a custom NanoString nCounter panel was designed. Alongside the Stem11 genes, the previously published LSC17 genes were included as an established transcriptional prognostic system for AML. For data normalization, seven housekeeping genes were further included from a previous custom NanoString nCounter panel. The full list of the 35 genes in our custom panel is provided in the manuscript."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted at MLL Munich Leukemia Laboratory and RNA integrity was assessed by TapeStation.","Scaning - Following hybridization, samples were processed using the NanoString nCounter Prep Station according to the manufacturer's instructions. Hybridized probe-target complexes were immobilized and aligned in the nCounter cartridge. Cartridges were scanned using the NanoString nCounter Digital Analyzer, which images fluorescent barcodes corresponding to individual reporter probes. Raw digital counts for each target transcript were extracted using the NanoString nCounter analysis software.","Sample Collection - Bone marrow samples were collected from de novo AML patients at diagnosis, prior to initiation of therapy.","Labeling - Target-specific reporter probe pairs were used as provided in the NanoString nCounter CodeSet.","Hybridization - RNA samples were hybridized to the Stem11 custom NanoString nCounter CodeSet. Hybridization buffer (70 µl) was added to each vial of the Reporter CodeSet, and 8 µl was added to each hybridization tube along with the RNA input and 2 µl of the Capture Probeset. Reactions were incubated at 65°C for 18 hours, then ramped down to 4°C. Samples were processed on the nCounter Prep Station within 24 hours using the High Sensitivity protocol, which removes excess probes and immobilizes hybridized samples in a sample cartridge. Cartridges were scanned on the nCounter Digital Analyzer."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Raw NanoString counts were obtained from RCC files generated by the NanoString nCounter Digital Analyzer. Data quality control and normalization were performed using standard NanoString procedures. Counts were first normalized using the geometric mean of positive control probes to correct for variation in hybridization efficiency and scanning. Background correction was applied based on negative control probes. Sample content normalization was then performed using the geometric mean of housekeeping genes included in the CodeSet to account for differences in RNA input. The resulting normalized counts were exported as a tab-delimited matrix for downstream analysis. Normalized counts were log2-transformed prior to downstream analysis."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["nCounter Prep Station & Digital Analyzer","N/A","TapeStation","NanoString"],"study_type":["transcription profiling by array"],"species":["Homo sapiens"],"pubmed_authors":["Bertie Gottgens","Rebecca Hannah","Nicola Wilson"],"additional_accession":[]},"is_claimable":false,"name":"Stem11 score: towards rapid clinical prognostication for acute myeloid leukemia","description":"As a rapid Stem11 scoring platform, a custom NanoString nCounter panel was designed. Alongside the Stem11 genes, the previously published LSC17 genes were included as an established transcriptional prognostic system for AML. For data normalization, seven housekeeping genes were further included from a previous custom NanoString nCounter panel. The full list of the 35 genes in our custom panel is provided in the manuscript.","dates":{"release":"2026-04-21T00:00:00Z","modification":"2026-04-21T08:32:27.526Z","creation":"2026-03-19T10:55:01.907Z"},"accession":"E-MTAB-16782","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"]}}