{"database": "metadata", "table": "run_metadata", "rows": [[32065, "SRR29007876", "SRX24534894", "SRS21280576", "SRP507323", "PRJNA1111056", "Increase in ER mitochondria contacts and mitochondrial fusion are hallmarks of mitochondrial activation during embryogenesis", "GSE267318", "Transcriptome Analysis", "Mitochondrial energy production is essential for development  yet the mechanisms underlying the continuous increase in mitochondrial activity during embryogenesis remain elusive. Using zebrafish as a model system for vertebrate development  we identify two sequentially acting mechanisms that could contribute to the rise in mitochondrial activity: an increased association between mitochondria and the endoplasmic reticulum ER at early stages  followed by the fusion of mitochondria leading to their elongated morphology at later embryonic stages. By comprehensively profiling mitochondrial activity  abundance  morphology  metabolome  proteome and phospho proteome as well as respiratory chain enzymatic activity  we find that the increase in mitochondrial activity during embryogenesis does not require mitochondrial biogenesis  is not limited by metabolic substrates at early stages  and occurs under steady levels of respiratory chain complexes and enzymatic activities. Instead  our analyses pinpoint a previously unexplored increase in mitochondrial ER association during early stages in combination with changes in mitochondrial morphology at later stages as possible contributors to the rise in mitochondrial activity during embryogenesis. Overall  our systematic profiling of the molecular and morphological changes to mitochondria during embryogenesis provides a valuable resource for further studying mitochondrial function during embryogenesis. Overall design: To investigate whether oligomycin treated embryos  we performed RNA seq experiment to detect ZGA genes. As a control we used untreated and  actinomycin injected embryos to block zygotic transcription.", null, null, null, "oligomycin 3h 239862", "GSM8263846", null, "source name:Embryo|tissue:Embryo|genotype:WT TLAB|treatment:oligomycin|time:3 hpf|geo loc name:missing|collection date:missing", "oligomycin 3h 239862", "Reads were preprocessed using umi2index Lexogen to add the UMI sequence to the read identifier  and trimmed using BBDuk v38.06 ref=polyA.fa.gz truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20. Reads mapping to abundant sequences mitochondrial chromosome  phiX174 genome  and silva zebrafish rRNAs from the SILVA rRNA database were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c  alignments were processed using collapse UMI bam Lexogen and reads in genes were counted with featureCounts subread v1.6.2 using strand specific read counting  s 1 . Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "Embryo", "Embryos were collected as soon as they were laid and put into E3 medium 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  10\u22125% methylene blue containing inhibitors. Embryos were kept in this medium for the duration of the experiment. For this experiment we used already established concentrations for inhibitors: oligomycin Millipore  495455 1\u00b5M  actinomycin D Sigma Aldrich  A1410 10\u00b5g/ml. Untreated embryos were kept alongside as controls.", "Total RNA was extracted using RNeasy Mini Kit Qiagen  175023525. 1.5\u00b5g of total RNA was used for the construction of sequencing libraries. Samples were submitted to VBCF NGS facility for library preparation and NGS sequencing. Samples were prepared with Quantseq kit Lexogen protocol.", "E3 medium 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  10\u22125% methylene blue.", "tissue:Embryo|genotype:WT TLAB|treatment:oligomycin|time:3 hpf", "GSM8263846", "GSM8263846: oligomycin 3h 239862; Danio rerio; RNA Seq", "GSM8263846 r1", "GSM8263846", "1", "Total RNA was extracted using RNeasy Mini Kit Qiagen  175023525. 1.5\u00b5g of total RNA was used for the construction of sequencing libraries. Samples were submitted to VBCF NGS facility for library preparation and NGS sequencing. Samples were prepared with Quantseq kit Lexogen protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP507323", null, "loader:fastq load.py", "239862_S44_R1_001.fastq.gz", "fastq", 964699000.0, 9646990.0, "GSM8263846 r1", "0:100", "A:356569674;C:145609333;G:187599003;T:274847064;N:73926", 100, null, null, null, 356569674, 145609333, 187599003, 274847064, 73926, "SRX24534894", "SRS21280576", "SRA1865615", "Pauli, IMP", "Pauli, IMP", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-05-13", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["32065"], "units": {}, "query_ms": 10.7275420014048}