biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIris Zhutranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-44175The 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 typebiostudies-arrayexpressNucleic 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.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsDavid LandsmanTao DengIris ZhuMichael BustinImage Adquisition - Scanning was performed with the Affymetrix GeneChip scanner using default settings.Assay Data Transformation - ID_REF = VALUE = normalized signal intensityFeature 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”falseExpression data from mouse embyonic stem cell, neural progenitor and neuronThe 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 type2013-02-09T00:00:00Z2023-08-26T17:38:38.739Z2022-02-07T23:29:29.107ZE-GEOD-44175GSE44175EFO_0002768