run_metadata: 69020

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
69020	SRR18305958	SRX14443372	SRS12250385	SRP363665	PRJNA815356	Gene expression data from lsd1 mutant zebrafish embryos	GSE198476	Transcriptome Analysis	Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.		pubmed:36594016		17656X11	GSM5949314		source name:tail/posterior to yolk sac\|age:24 hpf\|genotype:36433 mutant\|tissue:tail/posterior to yolk sac	17656X11	The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts	tail/posterior to yolk sac	Tails frozen at 80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.	Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598	Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.	age:24 hpf\|genotype:36433 mutant\|tissue:tail/posterior to yolk sac	GSM5949314	GSM5949314: 17656X11; Danio rerio; RNA Seq	GSM5949314 r1	GSM5949314	1	Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP363665		loader:fastq load.py	11R1.fastq.gz 11R2.fastq.gz	fastq fastq	7843778654.0	25972777.0	GSM5949314 r1	0:151 1:151	A:2038808042;C:1887346702;G:1979694397;T:1937559070;N:370443	151	151			2038808042	1887346702	1979694397	1937559070	370443	SRX14443372	SRS12250385	SRA1385506	Huntsman Cancer Institute	Oncological Sciences, University of Utah	2	0.89301	0.89144	0.21031	0.20901	0.71088	0.71455	0.53793	0.5369	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown		United States	2022-03-11	Pharyngula	Embryo	Tail	Multi-system