run_metadata: 72200

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
72200	SRR22306363	SRX18279947	SRS15772343	SRP408138	PRJNA902019	Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament	GSE218068	Transcriptome Analysis	Anterior segment dysgenesis ASD resulting in vision impairment stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM. POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development Tg[foxc1b:GFP] we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing		pubmed:37024546		Foxc1b 96hpf	GSM6734159		source name:Anterior Segment Mesenchyme\|tissue:Anterior Segment Mesenchyme\|cell line:Tg[foxc1b:GFP]\|genotype:AB\|developmental stage:96hpf	Foxc1b 96hpf	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files	Anterior Segment Mesenchyme		Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then their eyes were dissected and subsequently collected on ice before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:Anterior Segment Mesenchyme\|cell line:Tg[foxc1b:GFP]\|genotype:AB\|developmental stage:96hpf	GSM6734159	GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq	GSM6734159 r1	GSM6734159	1	Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then their eyes were dissected and subsequently collected on ice before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP408138		loader:fastq load.py	96hpf_B_S3_L002_I1_001.fastq.gz 96hpf_B_S3_L002_R1_001.fastq.gz 96hpf_B_S3_L002_R2_001.fastq.gz	fastq fastq fastq	19616344548.0	105464218.0	GSM6734159 r4	0:8 1:28 2:150	A:4455009353;C:3588592225;G:3922172348;T:3853423493;N:435281	8	28	150		4455009353	3588592225	3922172348	3853423493	435281	SRX18279947	SRS15772343	SRA1541630	Famulski, Biology, University of Kentucky	Famulski, Biology, University of Kentucky	1	0.92045		0.21078		0.80322		0.59961		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2022-11-15	Larval	Larval	Multi-tissue	Multi-system