{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Cao Lab"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15948"],"description":["This study aimed to determine whether human nuclear-encoded tRNAs can enter mitochondria and to assess their potential involvement in mitochondrial protein translation. We isolated cytoplasmic fractions, intact mitochondria, and mitoplasts from human HEK293T cells and performed small RNA sequencing to profile tRNAs and other small RNAs. The mitoplast samples enabled the distinction between RNAs associated with the mitochondrial surface and those localized within the mitochondrial interior. In parallel, mitochondrial ribosomes were purified from the mitochondrial fraction to obtain mitochondrial ribosome-associated tRNAs. This dataset enables the characterization of mitochondrial small RNAs, the assessment of nuclear-encoded tRNA localization within mitochondria, and the evaluation of their"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - AQRNA-seq optimized version, as detailed in the Methods section of this article, The original version is \\\"Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.  Nat Biotechnol 39, 978–988 (2021)\\\".","Nucleic Acid Extraction - Total small RNAs were isolated using the RNAiso for Small RNA reagent (Takara, Code No. 9753A) following the manufacturer’s protocol. Briefly, samples were homogenized in RNAiso reagent to ensure complete cell lysis and RNase inactivation. After incubation at room temperature for 10 min, one-fifth volume of chloroform was added, and the mixture was vigorously vortexed for 15 s and centrifuged at 12,000 × g for 15 min at 4 °C. The upper aqueous phase, containing small RNAs (20–200 nt), was carefully transferred to a new tube, and an equal volume of isopropanol was added to precipitate RNA. Following incubation for 10 min and centrifugation at 12,000 × g for 10 min at 4 °C, the RNA pellet was washed twice with 75% ethanol, air-dried briefly (2–5 min), and dissolved ","Sample Collection - Using the mitochondrial isolation and purification procedures described in the article, purified mitochondria and cytosolic fractions were obtained. Subsequently, the mitochondrial Ribo-seq technique detailed in the article was applied to isolate highly purified mitochondrial ribosome fractions, cytosolic ribosome fractions, as well as total cellular ribosome fractions.","Sequencing - Small RNAs (20–200 nt) were isolated using RNAiso for Small RNA (Takara, Code No. 9753A). Libraries were constructed with AQRNA-seq protocol (optimized version). Sequencing was performed on an Illumina NovaSeq-Xplus platform to generate 150 bp paired-end reads."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - To normalize sequencing depth across samples, raw read counts were adjusted according to total library size using a total-count normalization approach. Specifically, a constant scaling factor was applied to each sample such that all libraries were normalized to an equivalent total number of mapped reads. This procedure ensures that observed differences in read abundance reflect true biological variation rather than discrepancies in sequencing depth or library yield.","Sequence Alignment - Following QC, read 2 did not meet preset quality criteria, therefore, alignments and subsequent analyses were performed in single-end mode using read 1 exclusively(*_1.fq.gz)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of non coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Cao Lab"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of human 293T cell line mitochondrial small RNA transcriptome","description":"This study aimed to determine whether human nuclear-encoded tRNAs can enter mitochondria and to assess their potential involvement in mitochondrial protein translation. We isolated cytoplasmic fractions, intact mitochondria, and mitoplasts from human HEK293T cells and performed small RNA sequencing to profile tRNAs and other small RNAs. The mitoplast samples enabled the distinction between RNAs associated with the mitochondrial surface and those localized within the mitochondrial interior. In parallel, mitochondrial ribosomes were purified from the mitochondrial fraction to obtain mitochondrial ribosome-associated tRNAs. This dataset enables the characterization of mitochondrial small RNAs, the assessment of nuclear-encoded tRNA localization within mitochondria, and the evaluation of their","dates":{"release":"2026-08-27T00:00:00Z","modification":"2026-08-27T01:00:42.346Z","creation":"2025-11-01T17:13:29.32Z"},"accession":"E-MTAB-15948","cross_references":{"ENA":["ERP183496"],"EFO":["EFO_0003737","EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}