biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsCarl-Johan Rubintranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-33430ZBED6 is a novel transcription factor unique to placental mammals and has evolved from a domesticated DNA transposon. Here we further characterize the functional significance of ZBED6 based on transcriptome analysis of mouse myoblasts after Zbed6 silencing. ZBED6 appears as an important transcriptional regulator since differential expression of more than 1,000 transcripts was consistently observed after Zbed6 silencing and these changes correlated with increased myotube formation. Up-regulated genes were associated with muscle contractile fibers and muscle organ development, while down-regulated genes were associated with ribosome function. Thirty-four small nucleolar RNAs showed differential expression and all increased in expression after Zbed6 silencing. This is particularly interestingbiostudies-arrayexpressNucleic Acid Extraction - RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.Labeling - Biotinylated probes were prepared from 250 ng of total RNA, using the Ambion Illumina TotalPrep RNA Amplification kitSample Processing - Cells were seeded in complete DMEM lacking antibiotics and reverse transfected with siRNA by lipofectamine 2000 (Invitrogen). ZBED6 silencing and validation of silencing was done by qPCR and western blotting as described (Markljung et al. 2009). Briefly, C2C12 cells were treated with ZBED6 or scrambled siRNAs for two days and four days in biological triplicates. Total RNA from each sample was extracted for qRT-PCR validation and microarray analysis.Growth Protocol - The C2C12 cells used for these studies were between passages 10 and 18. Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with L-glutamine (ATCC), supplemented with 10 % heat-inactivated fetal bovine serum and penicillin (0.2 U/mL)/streptomycin (0.2 μg/ml)/L-glutamine (0.2 μg/ml) (Gibco) at 37°C in a 5 % CO2 humidified atmosphere. At 70-80 % confluency, cells were trypsinized and seeded at 100,000 cells per well in 12-well plates (Falcon) for the transfection experiments.Hybridization - Standard Illumina hybridization protocolMIAME ScoreOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsCarl-Johan RubinFeature Extraction - The data were normalised using the lumi package implemented in the software FlexArray v. 1.4.1 using Robust spline normalizationAssay Data Transformation - ID_REF = <br>VALUE = Robust spline normalization<br>Detection Pval =Image Adquisition - Standard Illumina scanning protocolfalseUnraveling the role of ZBED6 in transcriptional regulation by whole transcriptome analysis after RNAi in mouse myoblastsZBED6 is a novel transcription factor unique to placental mammals and has evolved from a domesticated DNA transposon. Here we further characterize the functional significance of ZBED6 based on transcriptome analysis of mouse myoblasts after Zbed6 silencing. ZBED6 appears as an important transcriptional regulator since differential expression of more than 1,000 transcripts was consistently observed after Zbed6 silencing and these changes correlated with increased myotube formation. Up-regulated genes were associated with muscle contractile fibers and muscle organ development, while down-regulated genes were associated with ribosome function. Thirty-four small nucleolar RNAs showed differential expression and all increased in expression after Zbed6 silencing. This is particularly interesting2011-11-04T00:00:00Z2023-08-31T12:53:54.026Z2022-03-15T10:31:20.774ZE-GEOD-33430GSE33430EFO_0002768