{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Single Cell Omics Platform CBMR"],"organism":["Mus musculus"],"software":["nf-core/rnaseq v3.11.2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17577"],"description":["Transcriptome from immortalized murine brown adipocytes BMC. Cells were transfected with siRNA construct #1 or construct #2 (pool) or non-targeting control on day 3 of differentiation and harvested on day 7 of differentiation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Media was changed 2 days after transfection and cells were harvested or assayed on day 7 of the differentiation.","Sample Treatment - On day 3 of differentiation, cells were reverse transfected. In brief, siRNA targeting the gene of interest or relevant control siRNA were diluted in Opti-MEM (Gibco, 51985) to a final concentration of 300 nM. RNAiMAX (Invitrogen, 13778-150) was added to a final concentration of 30 μl/ml. The siRNA mix was added to the bottom of the wells in the plate-format of interest and allowed to incubate at RT for 30 min. In the meantime, cells were trypsinized, counted, and resuspended in culture media. Finally, the cell suspension was distributed on top of the siRNA mix to a final siRNA concentration of 50 nM.","Growth Protocol - Preadipocytes were cultured in basal DMEM (Gibco, 31966) containing 10% FBS (Sigma-Aldrich, F7524) and 1% penicillin/streptomycin. Cells were passaged when they reached 60-70% of confluence. Media was changed every 2nd day. On the day of 100% confluency, cell differentiation was induced by supplementing of standard media with the differentiation cocktail (insulin (20 nM) (Sigma-Aldrich, I9278), dexamethasone (1 mM) (Sigma-Aldrich, D1756), rosiglitazone (0.5 mM) (Cayman Chemicals, 71740), T3 (1 nM) (Sigma Aldrich, T6397), and 3-isobutyl-1-methylxanthine (IBMX) (250 μM) (Sigma-Aldrich, I5879)). On day 2 of differentiation, media was switched to maintenance media containing insulin and T3. Maintenance media was changed every 2nd day. Cells were harvested or assayed on day 7 of differentiation. The cells were maintained at 37°C in a humidified atmosphere with 5% CO2.","Nucleic Acid Extraction - polyadenylated mRNA was isolated from 1 μg of total RNA by incubation with oligo-dT beads and prepared according to manufacturer’s protocol (TrueSeq 2, Illumina). Isolated RNA was treated with DNase I (NEBM0303L) by mixing 250 ng of RNA, 8 Units of DNase I and DNase buffer in 10 µl reaction volume per sample and incubation the reaction mix for 15 min at 37 °C. Reaction was quenched by thorough vortexing of the samples and incubation at 85 °C for 5 min.","Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 platform using SP 100-cycle v1.5 reagents, generating 52-bp paired-end reads. Libraries were sequenced at a molarity of 2 nM with a 1% PhiX spike-in control.","Library Construction - mRNA-seq libraries were prepared using the Universal Plus mRNA-seq library preparation kit with NuQuant (TECAN, Männedorf, Switzerland, Cat. #M01485 V8) according to the manufacturer’s instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - FASTQ files were analyzed using nf-core/rnaseq v3.11.2 with the parameters --with_umi, --skip_umi_extract, and --umitools_umi_separator \\\":\\\", using the Mus musculus GRCm38 reference genome, and Ensemble gene model release 108.","Data Transformation - Uploaded data is raw reads, each row is a gene and each column is a sample. No normalization has been performed."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["Mitochondrial carrier SLC25A34 links clock, diet, and temperature control of adipocyte lipid cycling"],"pubmed_authors":["Iuliia Karavaeva, Astrid Linde Basse, Samuel A. J. Trammell, Mohammed Faiz Hussain, Lasse Kruse Markussen, Jesper F. Havelund, Marie Sophie Isidor, Adam Chatoff, Andrea A. Huacachino, Hannah J. Richter, Meghna Birla, Sabina Chubanava, Yann Deleye, Rini Arianti, David Tandio, Sarah E. Utzon, Zafir Kaiser, Yachen Shen, Ditte Neess, Hannes Embring, Dilip Menon, Olivia J. Conway, Frederike Sass, Fabian Finger, Lidia Argemi-Muntadas, Tao Ma, Elahu G. Sustarsic, Cecilie Kynding Kristensen, Rebecca L. McIntyre, Genesee J. Martinez, Anna Sofie Husted, Matthew J. Emmett, Zachary A. Kipp, Mikkel Frost, Mark P. Jedrychowski, Michel van Weeghel, Homa Majd, Ekaterina Zhuravleva, Robert W. McGarrah, Kaja Plucińska, Mohit K. Midha, Andreas Prokesch, Paul Cohen, James G. Granneman, Patrick Seale, Riekelt H. Houtkooper, Jacob B. Hansen, Steven P. Gygi, Thue W. Schwartz, Matthew P. Gillum, Terry D. Hinds, Jr., Raymond E. Soccio, Phillip J. White, Edmund R. S. Kunji, Thomas Moritz, Jonas T. Treebak, Endre Kristóf, Susanne Mandrup, Brice Emanuelli, Nathaniel W. Snyder, Daniel J. Fazakerley, Lawrence Kazak, Nils J. Færgeman, Mitchell A. Lazar, Zachary Gerhart Hines,","Iuliia Karavaeva","Single Cell Omics Platform CBMR","Zachary Gerhart-Hines"],"additional_accession":[]},"is_claimable":false,"name":"Mitochondrial carrier SLC25A34 links clock, diet, and temperature control of adipocyte lipid cycling","description":"Transcriptome from immortalized murine brown adipocytes BMC. Cells were transfected with siRNA construct #1 or construct #2 (pool) or non-targeting control on day 3 of differentiation and harvested on day 7 of differentiation.","dates":{"release":"2026-09-23T00:00:00Z","modification":"2026-09-23T13:39:12.395Z","creation":"2026-08-25T15:27:55.276Z"},"accession":"E-MTAB-17577","cross_references":{"ENA":["ERP204244"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}