run_metadata: 34150

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
34150	SRR31364128	SRX26737881	SRS23227902	SRP545529	PRJNA1186739	Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish	GSE282061	Transcriptome Analysis	The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural transcriptomic mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages different fin positions or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry and analyzed by 10x scRNA seq.		pubmed:40305763		dataset1 stages rep3	GSM8635050		source name:dorsal fin\|tissue:dorsal fin\|genotype:wild type\|geo loc name:missing\|collection date:missing	dataset1 stages rep3	We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS	dorsal fin		Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle high output kits read 1: 26 cycles i7 Index: 8 cycles read 2: 57 cycles.		tissue:dorsal fin\|genotype:wild type	GSM8635050	GSM8635050: dataset1 stages rep3; Danio rerio; RNA Seq	GSM8635050 r1	GSM8635050	1	Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle high output kits read 1: 26 cycles i7 Index: 8 cycles read 2: 57 cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550		SRP545529		loader:fastq load.py	dorsal_3_S3_L001_I1_001.fastq.gz dorsal_3_S3_L001_R1_001.fastq.gz dorsal_3_S3_L001_R2_001.fastq.gz	fastq fastq fastq	2602160384.0	28284352.0	GSM8635050 r1	0:8 1:28 2:56	A:469841004;C:333542050;G:367823398;T:412316065;N:401195	8	28	56		469841004	333542050	367823398	412316065	401195	SRX26737881	SRS23227902	SRA2016042	UVA	UVA												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Unknown	2024-11-15	Undetermined	Embryo	Fin	Surface Structure