{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Iris Zhu"],"study_type":["transcription profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-44175"],"description":["The effect of HMGN1 protein on gene expression of mouse ESC, NP and Neurons were investigated by comparing the transcriptome between Hmgn1+/+ and Hmgn1 -/- cells. three cell types, two genotypes, three reps per sample type"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated by RNeasy Mini Kit (Qiagen) followed by “on-column” DNase I treatment according to the manufacturer's instructions.","Growth Protocol - The ES cells were co-cultured with mitomycin-c treated mouse primary embryonic fibroblast feeders or cultured under feeder-free conditions, they were maintained in Knock-out Dulbecco’s modified Eagle’s medium, with 20% serum replacement, 0.055 mM β-mercaptoethanol, 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5000 U/ml penicillin/streptomycin, and 1000 U/ml LIF. In vitro differentiation of ES cells along neural lineage was performed using the Mouse Dopaminergic Neuron Differentiation Kit (R&D System) according to the manufacturer’s instruction.","Hybridization - Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.","Labeling - Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["David Landsman","Tao Deng","Iris Zhu","Michael Bustin"],"data_protocol":["Image Adquisition - Scanning was performed with the Affymetrix GeneChip scanner using default settings.","Assay Data Transformation - ID_REF =  VALUE = normalized signal intensity","Feature Extraction - All analysis was performed using R and BioConductor. Expression levels were derived using the Robust Multichip Average (RMA) protocol with default setting and differentially expressed genes were identified using an empirical Bayes method implemented in the R package “Limma”"],"additional_accession":[]},"is_claimable":false,"name":"Expression data from mouse embyonic stem cell, neural progenitor and neuron","description":"The effect of HMGN1 protein on gene expression of mouse ESC, NP and Neurons were investigated by comparing the transcriptome between Hmgn1+/+ and Hmgn1 -/- cells. three cell types, two genotypes, three reps per sample type","dates":{"release":"2013-02-09T00:00:00Z","modification":"2023-08-26T17:38:38.739Z","creation":"2022-02-07T23:29:29.107Z"},"accession":"E-GEOD-44175","cross_references":{"GEO":["GSE44175"],"EFO":["EFO_0002768"]}}