run_metadata: 26510

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
26510	SRR26038419	SRX21755507	SRS18862354	SRP459901	PRJNA1015602	mTOR promotes zebrafish larvae fin regeneration through regulating macrophages activation and CaM mTOR dnm1l axis	GSE242949	Transcriptome Analysis	To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout mTOR KO transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover mTOR was essential for the activation of macrophages which is a key factor in maintaining the regenerative repair process. We also demonstrated that mTOR knockdown attenuated the proliferative capacity of bud embryo cell during the regenerative phase while cell apoptosis was not affected. RNA sequence analysis showed changes in mitochondrial function and dnm1l was identified as the main regulatory factor during the fin regeneration stage. We further suggested that mTOR may promote mitochondrial fission to support bud embryo cell regeneration via CaM mTOR dnm1l axis. Overall design: Sequencing samples for the micro transcriptome were obtained from tail fin tissues regenerated for 24 h. Fifty regenerated tail fins were extracted for each sample from the control and experimental groups treated with 1 uM Rapamycin. Each group had 3 biological replicates and samples were lysed using Trizol. Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd Hangzhou China.		pubmed:38812038		ctrl1	GSM7775457		source name:larvae fin\|tissue:larvae fin\|genotype:WT\|treatment:DMSO\|geo loc name:missing\|collection date:missing	ctrl1	Raw data quality control Reference genome alignment Transcript assembly Read count extration and normalization DEGs analysis Assembly: mm10	larvae fin		SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB M0348S by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand indexed Y adapters are ligated to the fragments and the ligated products are amplified with PCR.		tissue:larvae fin\|genotype:WT\|treatment:DMSO	GSM7775457	GSM7775457: ctrl1; Danio rerio; RNA Seq	GSM7775457 r1	GSM7775457	1	SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. cDNA was fragmented by dsDNA Fragmentase NEB M0348S by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt end DNA fragments are generated using a combination of fill in reactions and exonuclease activity and size selection is performed with provided sample purification beads. An A base is then added to the blunt ends of each strand indexed Y adapters are ligated to the fragments and the ligated products are amplified with PCR.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP459901		loader:fastq load.py	ctrl1_Clean_Data1.fq.gz ctrl1_Clean_Data2.fq.gz	fastq fastq	5342798577.0	18260213.0	GSM7775457 r1	0:146.40 1:146.19	A:1434645762;C:1243936102;G:1249988331;T:1414082855;N:145527	146	146			1434645762	1243936102	1249988331	1414082855	145527	SRX21755507	SRS18862354	SRA1710567	Chongqing Medical University	Chongqing Medical University	2	0.95229	0.95004	0.06613	0.06596	0.71086	0.71303	0.47912	0.47827	149	149	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		China	2023-09-12	Larval	Larval	Fin	Surface Structure