{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan Dobeš"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15468"],"description":["The goal of the experiment is to determine the impact of Claudin 1 deficiency on the gene expression of thymic type 1 dendritic cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - ibraries were sequenced with the NextSeq P2 XLEAP-SBS Reagent Kit on a NextSeq 2000 sequencer (Illumina). Pair-end: rd1=75bp, rd2=15bp.","Nucleic Acid Extraction - Complete mRNA was isolated based on polyA selection using Dynabeads mRNA direct purification kit.","Library Construction - Sequencing libraries were prepared using the MARS-seq protocol, as described previously (Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–779 (2014)).","Sample Collection - The Defa6-iCre R26-TdTomato mouse model, which exhibits restricted expression of the TdTomato fluorescent protein in medullary thymic epithelial cells, was used as the recipient for competitive bone marrow chimeras composed of Claudin-1–sufficient and Claudin-1–deficient donor cells. After six weeks, thymi were dissected and type 1 dendritic cells arising from Claudin-1–sufficient and Claudin-1–deficient bone marrow were isolated by flow cytometric sorting from one individual animal. Cells were directly sorted into lysis buffer."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200).  Reads were mapped to genome using STAR (DOI: 10.1093/bioinformatics/bts635) v2.7.10a.  The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):  We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) v2.0.2 in union mode.  Further analysis is done for genes having minimum 5 read in at least one sample. The analysis was done using UTAP:  Kohen R, Barlev J, Hornung G, Stelzer G, Feldmesser E, Kogan K, Safran M, Leshkowitz D: UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics 2019, 20(1):154.","Data Transformation - Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) v1.36.0 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg (DOI: 10.1111/j.2517-6161.1995.tb02031.x)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Jan Dobeš"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq analysis of murine thymic type 1 dendritic cells from competitive bone marrow chimeras containing both claudin-1–deficient and claudin-1–sufficient cells","description":"The goal of the experiment is to determine the impact of Claudin 1 deficiency on the gene expression of thymic type 1 dendritic cells.","dates":{"release":"2025-08-08T00:00:00Z","modification":"2025-08-08T15:47:57.771Z","creation":"2025-08-08T15:35:50.325Z"},"accession":"E-MTAB-15468","cross_references":{"ENA":["ERP178572"],"Biostudies":["E-MTAB-14319"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}