run_metadata: 55222

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
55222	SRR10182210	SRX6902835	SRS5434732	SRP223244	PRJNA574059	Cellular diversity of the regenerating caudal fin	GSE137971	Transcriptome Analysis	single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies filtered through 40 µm cell strainers and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging alignment to zebrafish reference genome GRCz10 and feature counting based on Ensembl release 91 cellranger count.		pubmed:32851162		preinjury fin2 scRNA	GSM4095394		source name:Preinjury caudal fin\|strain:Tgsp7:egfp\|age:1 year\|tissue:caudal fin\|timepoint:preinjury	preinjury fin2 scRNA	All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.	Preinjury caudal fin		We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics	Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility with system water temperature at 28.5˚C and a day night cycle controlled as 14 hr light/10 hr dark.	strain:Tgsp7:egfp\|age:1 year\|tissue:caudal fin\|timepoint:preinjury	GSM4095394	GSM4095394: preinjury fin2 scRNA; Danio rerio; RNA Seq	GSM4095394		1	We anesthetized one year old fish with 0.16g/L MS 222 in system water and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT filtered through 40µm cell strainers and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics	GEO Accession:GSM4095394	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP223244			samp2_S2_L002_R2_001.fastq.gz samp2_S2_L002_R1_001.fastq.gz	fastq fastq	14313306001.0	141715901.0	GSM4095394 r1	0:26 1:75	A:4080921082;C:3121900376;G:3341495424;T:3761528384;N:7460735	26	75			4080921082	3121900376	3341495424	3761528384	7460735	SRX6902835	SRS5434732	SRA968154	GEO	Ting Wang, Genetics, Washington University St Louis	2	0.0029	0.89943	0.00115	0.07948	0.99543	0.8714	0.29607	0.47916	26	75	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2019-09-25	Adult	Adult	Fin	Surface Structure