{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Neil Morgan"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15572"],"description":["To identify the mechanism through which SLFN14 may regulate megakaryopoiesis and platelet function, we performed RNA sequencing analysis to define alterations in gene activity arising as a result of conditionally knocking down Slfn14 in vivo. Bulk RNA-sequencing was performed on total RNA extracted from mature murine Slfn14fl/flPF4-Cre derived MKs and peripheral blood platelets and compared to Slfn14+/+PF4-Cre control MKs/platelets. All individual samples were run in triplicate and normalised before comparisons between each SLFN14 mutant."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Illumina/NEB kit protocol - Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina with NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) according to the manufacturer’s protocol. During this process, the libraires were indexed using NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) Set 4. The prepared libraries were quantified via a fluorometric method involving a Promega QuantiFluor dsDNA assay and qualified using electrophoretic separation on the Agilent TapeStation 4200.","Sample Collection - Mice were exsanguinated under terminal anesthesia by isoflurane/O2 (5%) gas. Blood was drawn from the inferior vena cava, using a 25-gauge needle, into 1:10 (volume-to-volume ratio) acid citrate dextrose anticoagulant.","Sequencing - Sequencing was performed using the Illumina HiSeq 4000.","Nucleic Acid Extraction - Platelets and megakaryocytes were isolated and RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNA sequencing performed on platelet and MK RNA in triplicate groups from individual mice (Slfn14fl/flPF4-Cre, Slfn14f+/+PF4-Cre) and normalised comparing mutant and WT groups"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Neil Morgan"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq shows genes enhanced in translation and transcription pathways in MKs and platelets from Slfn14fl/flPF4-Cre mouse model","description":"To identify the mechanism through which SLFN14 may regulate megakaryopoiesis and platelet function, we performed RNA sequencing analysis to define alterations in gene activity arising as a result of conditionally knocking down Slfn14 in vivo. Bulk RNA-sequencing was performed on total RNA extracted from mature murine Slfn14fl/flPF4-Cre derived MKs and peripheral blood platelets and compared to Slfn14+/+PF4-Cre control MKs/platelets. All individual samples were run in triplicate and normalised before comparisons between each SLFN14 mutant.","dates":{"release":"2025-09-29T00:00:00Z","modification":"2026-05-28T10:15:20.661Z","creation":"2025-09-12T14:40:47.614Z"},"accession":"E-MTAB-15572","cross_references":{"ENA":["ERP180028"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}