{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Celine Delucinge Vivier"],"organism":["Mus musculus"],"software":["MicroArraySuite 5.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-TABM-677"],"description":["To reveal changes in chromatin state and correlate with transcriptional activity during embryonic development"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - cDNA Synthesis: GeneChip Two-Cycle cDNA Synthesis Kit (Affymetrix) ; cDNA Cleanup: Affymetrix GeneChip Sample Cleanup Module ; cRNA Synthesis: Affymetrix GeneChip Expression 3'-Amplification Kit for IVT Labeling ; cRNA Cleanup: Affymetrix GeneChip Sample Cleanup Module ; Spike Target Element: mRNA+Target ; Spiking Control: Affymetrix standard ; Dye: biotin","Nucleic Acid Extraction - Nucleic Acid Extraction Method: Qiagen RNeasy Micro Columns ; Nucleic Acid Type: total_RNA ; Nucleic Acid Cleanup: Qiagen RNeasy Micro Kit ; Amplification Method: No amplification","Labeling - cRNA Synthesis: not appliable ; cRNA Cleanup: not appliable ; Spike Target Element: Target ; Spiking Control: Affymetrix standard ; Dye: biotin","Hybridization - Washing/Staining Procedure: FS450_0002 ; Washing/Staining Instrumentation: Fluidics Station 450","Nucleic Acid Extraction - Nucleic Acid Extraction Method: phenol-based method ; Nucleic Acid Type: DNA ; Nucleic Acid Cleanup: phenol-based method ; Amplification Method: PCR","Growth Protocol - E14 mouse ES cells were grown under feeder-free conditions on gelatinized plates in Dulbeccoï¾'s modified Eagleï¾'s medium (DMEM) supplemented with 15% fetal calf serum, 2 mM L-glutamine, 1x non-essential amino acids (GIBCO), 0.1 mM b-mercaptoethanol, 40 mg/ml Gentamycine and 1000 U/ml LIF."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Additional Files","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - Title: Affymetrix CEL analysis. Description:"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["During vertebrate development, the temporal control of Hox gene transcriptional activation follows the genomic order of the genes within the Hox clusters. Although it is recognized that this \"Hox clock\" serves to coordinate body patterning, the underlying mechanism remains elusive. We have shown that successive Hox gene activation in the mouse embryo is closely associated with a directional transition in chromatin status, as judged by the dynamic progression of transcription-competent modifications: Increases in activation marks correspond to decreases in repressive marks. Furthermore, using a mouse in which a Hox cluster was split into two pieces, we document the necessity to maintain a clustered organization to properly implement this process. These results suggest that chromatin modific"],"study_type":["ChIP-chip by array"],"species":["Mus musculus"],"pubmed_title":["Epigenetic Temporal Control of Mouse Hox Genes in Vivo"],"pubmed_authors":["Soshnikova, Natalia; Duboule, Denis","Natalia Soshnikova","Celine Delucinge Vivier"],"additional_accession":[]},"is_claimable":false,"name":"Chromatin immunoprecipitation of mouse embryonic stem cells, mesenchymal/neuronal progenitors and hepatocytes to identify epigenetic control of HOX gene termporal regulation","description":"To reveal changes in chromatin state and correlate with transcriptional activity during embryonic development","dates":{"release":"2009-06-05T00:00:00Z","modification":"2022-11-23T00:25:27.932Z","creation":"2022-03-09T13:19:23.507Z"},"accession":"E-TABM-677","cross_references":{"pubmed":["19498168"],"EFO":["EFO_0002760"],"doi":["19498168"]}}