{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Pekka Rappu"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15210"],"description":["To study function of Embigin in mouse embryos, five E17.5 WT and Emb-/- kidneys were dissected, and the RNA was isolated and submitted to high-throughput sequencing to find differentially expressed genes between WT and Emb knock-out mouse lungs or placentas"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was performed with NovaSeq 6000 SP Sequencing System (Illumina) using paired-end sequencing chemistry and 2 x 50 bp read length. The reads obtained from the instrument were base called using bcl2fastq2 conversion software. Raw data were obtained as fastq-files.","Library Construction - The libraries were prepared from 300 ng of RNA from each sample using TruSeq Stranded mRNA HT Kit and TruSeq Stranded mRNA Sample Preparation protocol 15031047 (Illumina)","Sample Collection - Five E17.5 Wild type and Emb-/- mouse kidneys were dissected.","Nucleic Acid Extraction - Total RNA was isolated by using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The reads were aligned against the reference genome (Mus musculus GRCm38.95, available in Chipster) using STAR, version 2.7.3 (Dobin et al., 2013)","Data Transformation - The reads associated with each gene were counted using the HTSeq package, version 0.12.4."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Pekka Rappu","Jyrki Heino"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of E17.5 WT and Emb-/- kidney","description":"To study function of Embigin in mouse embryos, five E17.5 WT and Emb-/- kidneys were dissected, and the RNA was isolated and submitted to high-throughput sequencing to find differentially expressed genes between WT and Emb knock-out mouse lungs or placentas","dates":{"release":"2026-02-10T00:00:00Z","modification":"2026-02-10T06:43:52.045Z","creation":"2025-06-09T10:49:22.337Z"},"accession":"E-MTAB-15210","cross_references":{"ENA":["ERP173275"],"Biostudies":["E-MTAB-10641"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}