{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13335"],"description":["Analysis of global variability of translation initiation between the Eif6 WT control genotype and the Eif6 S235A mutated MEF lines pre-treated with harringtonine. Ribosome Protected Fragments (RPFs) were obtained following the method reported in Ingolia NT et al., NatProtoc 2012. (doi:10.1038/nprot.2012.086)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Immagina Biotechnology LACEseq #LS-001_12","Nucleic Acid Extraction - Cells were lysed in 20mM Tris-HCl, 50mM NaCl, 10mM MgCl2, 1mM DTT, 100ug/ml cyclohexamide, 1% NP-40, 0.2mg/ml heparin. Ribosome Protected Fragments (RPF) were obtained following Ingolia 2017 (10.1016/j.ymeth.2017.05.028).","Sample Collection - Immortalized MEF cells were pre-treated with 2ug/ml harringtonine for 2 minutes followed by 100ug/ml cyclohexamide for other 2 minutes. Finally, the cells were washed once with ice-cold PBS 10ug/ml cyclohexamide.","Sequencing - 500 pM library, Phix 10%, NextSeq 1000/2000 P2 100 cycles Illumina Kit, sequenced with NextSeq 2000"],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - The raw fastq files underwent trimming and UMI extraction as reported in the Laceseq kit guidelines. Reads aligning to tRNAs and ncRNAs were removed using bowtie2"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["Ribo-seq"],"species":["Mus musculus"],"additional_accession":["ERP151032"],"pubmed_authors":["Ivan Ferrari"]},"is_claimable":false,"name":"Ribo-seq of Eif6 WT and Eif6 S235A Mouse Embryonic Fibroblasts (MEFs) pre-treated with harringtonine","description":"Analysis of global variability of translation initiation between the Eif6 WT control genotype and the Eif6 S235A mutated MEF lines pre-treated with harringtonine. Ribosome Protected Fragments (RPFs) were obtained following the method reported in Ingolia NT et al., NatProtoc 2012. (doi:10.1038/nprot.2012.086)","dates":{"release":"2026-02-10T00:00:00Z","modification":"2026-05-27T12:52:57.877Z","creation":"2023-09-11T15:13:32.158Z"},"accession":"E-MTAB-13335","cross_references":{"ENA":["ERP151032"],"EFO":["EFO_0002944","EFO_0004170","EFO_0008891","EFO_0005518","EFO_0003816","EFO_0004184"]}}