{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Shiyu Bian"],"organism":["Homo sapiens"],"software":["Trimmomatic v0.36, STAR v2.5.2b, featureCounts (Subread v1.5.2), DESeq2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17070"],"description":["Mitochondrial DNA mutations in components of the electron transport chain disrupt mitochondrial activity and can alter how cells take up and utilize nutrients. To investigate how mtND6 (Complex I) mutations reshape the transcriptional profile of human pluripotent stem cells, we performed bulk RNA sequencing on hESCs carrying levels of mtND6 mutations: wild-type, 5%, 56%, and 77% heteroplasmy. All four lines were profiled in mTeSR+, and wild-type and 77% mutant hESCs were additionally profiled in Essential 8 (E8) medium to identify transcriptional changes robust to differences in culture nutrient composition. Each sample was sequenced in biological triplicate (n = 18). Total RNA was poly(A)-selected, and libraries were sequenced on an Illumina NovaSeq platform, paired-end read, 20 million reads per sample."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on an Illumina NovaSeq instrument in paired-end mode with a read length of 2×150 bp at Azenta Life Sciences. Approximately 20 million paired-end reads were generated per sample.","Sample Collection - Cells were grown to 70-80% confluency, washed twice with PBS, and dissociated using ReleSR. Cell pellets were collected by centrifugation at 300 × g for 5 minutes at 4°C, snap-frozen in dry ice, and stored at -80°C until RNA extraction. For each biological replicate, an independent passage of cells was harvested.","Library Construction - RNA-seq libraries were prepared by Azenta Life Sciences using a poly(A) selection-based mRNA library preparation workflow. Briefly, mRNA was enriched from total RNA by poly(A) selection, fragmented, and reverse transcribed using random hexamer priming. First and second strand cDNA were synthesized, followed by end repair, 5' phosphorylation, and dA-tailing. Sequencing adapters were ligated, and libraries were PCR-enriched. Library quality and quantity were assessed prior to sequencing.","Nucleic Acid Extraction - Total RNA was extracted from cell pellets using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific). RNA samples were then shipped to Azenta Life Sciences for quality assessment and library preparation.","Growth Protocol - Human embryonic stem cells (H1 / WA01) carrying different levels of mtND6 mutations (wild-type, 5%, 56%, and 77%) were generated by mitochondrial base editing using DdCBE (Mok et al., 2020). Cells were maintained on Geltrex-coated plates (Thermo Fisher Scientific) in either mTeSR+ medium (STEMCELL Technologies) or in-house prepared Essential 8 (E8) medium at 37°C in a humidified incubator with 5% CO2. Medium was changed daily, and cells were passaged every 4-5 days using ReleSR. Cells were harvested at approximately 70-80% confluency for RNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v0.36. Trimmed reads were aligned to the Homo sapiens GRCh38 reference genome (Ensembl) using the STAR aligner v2.5.2b. Gene-level read counts were obtained using featureCounts from the Subread package v1.5.2, counting only unique reads that fell within exon regions, using the gene_id feature in the annotation file. Differential expression analysis was performed using DESeq2 in R, applying median-of-ratios normalization and the Wald test for significance. Genes with an adjusted p-value < 0.05 (Benjamini-Hochberg) and |log2 fold change| > 1 were considered differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was performed using DAVID."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","Nanodrop"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_authors":["Shiyu Bian","Tristan Rodriguez"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq profiling of human embryonic stem cells carrying different levels of mtDNA heteroplasmy cultured in mTeSR Plus and E8 media.","description":"Mitochondrial DNA mutations in components of the electron transport chain disrupt mitochondrial activity and can alter how cells take up and utilize nutrients. To investigate how mtND6 (Complex I) mutations reshape the transcriptional profile of human pluripotent stem cells, we performed bulk RNA sequencing on hESCs carrying levels of mtND6 mutations: wild-type, 5%, 56%, and 77% heteroplasmy. All four lines were profiled in mTeSR+, and wild-type and 77% mutant hESCs were additionally profiled in Essential 8 (E8) medium to identify transcriptional changes robust to differences in culture nutrient composition. Each sample was sequenced in biological triplicate (n = 18). Total RNA was poly(A)-selected, and libraries were sequenced on an Illumina NovaSeq platform, paired-end read, 20 million reads per sample.","dates":{"release":"2026-06-06T00:00:00Z","modification":"2026-06-06T01:01:10.432Z","creation":"2026-05-21T14:48:48.388Z"},"accession":"E-MTAB-17070","cross_references":{"ENA":["ERP193680"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184"]}}