run_metadata: 32061

This data as json

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
32061	SRR29007872	SRX24534898	SRS21280580	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.				untreated 3h 239870	GSM8263850		source name:Embryo\|tissue:Embryo\|genotype:WT TLAB\|treatment:untreated\|time:3 hpf\|geo loc name:missing\|collection date:missing	untreated 3h 239870	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 10−5% 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 1µM actinomycin D Sigma Aldrich A1410 10µg/ml. Untreated embryos were kept alongside as controls.	Total RNA was extracted using RNeasy Mini Kit Qiagen 175023525. 1.5µg 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 10−5% methylene blue.	tissue:Embryo\|genotype:WT TLAB\|treatment:untreated\|time:3 hpf	GSM8263850	GSM8263850: untreated 3h 239870; Danio rerio; RNA Seq	GSM8263850 r1	GSM8263850	1	Total RNA was extracted using RNeasy Mini Kit Qiagen 175023525. 1.5µg 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000		SRP507323		loader:fastq load.py	239870_S36_R1_001.fastq.gz	fastq	1093077000.0	10930770.0	GSM8263850 r1	0:100	A:401209579;C:172475514;G:213719175;T:305590035;N:82697	100				401209579	172475514	213719175	305590035	82697	SRX24534898	SRS21280580	SRA1865615	Pauli, IMP	Pauli, IMP												B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	lexogen	bulk	unknown	unknown		Austria	2024-05-13	Blastula	Embryo	Embryo Imprecise	All anatomical structures