{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Carolin Schmidtke"],"study_type":["transcription profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-5706"],"description":["Obtain insight into lysosomal signaling pathways"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - For hybridisation, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) is used. 600 ng of each cRNA is hybridised on 8x60K microarrays at 65 °C for 17 h using Agilent's recommended hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37 °C) Gene Expression Wash Buffer 2 for one minute.","Labeling - For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate  fluorescent cRNA. For 1st strand synthesis, a random primer / oligo-dT primer mixture is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed.","Growth Protocol - cerebellar cells were grown on 3.5 cm plates in DMEM supplemented with 10 % FCS, 1x GlutaMax, 1x PenStrep, 24 mM KCl at 33 °C, 5 % CO2","Nucleic Acid Extraction - RNA was isolated using Qiagen RNeasy columns according to the manufacturer's instructions","Sample Collection - cells were washed two times with PBS on ice and lysed directly on the plate in RNA lysis buffer from Qiagen according to the manufacturer's instructions"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Carolin Schmidtke"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptional profiling of Cln3 mutant cerebellar cell line against wild-type","description":"Obtain insight into lysosomal signaling pathways","dates":{"release":"2022-12-30T00:00:00Z","modification":"2022-01-31T19:49:37.726Z","creation":"2022-01-31T19:49:37.726Z"},"accession":"E-MTAB-5706","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003813","EFO_0003789","EFO_0005518","EFO_0003815"]}}