run_metadata: 30586

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
30586	SRR27848608	SRX23511536	SRS20362004	SRP487839	PRJNA1072736	Transgenic tools targeting striatal and pallidal subpopulations reveal both evolutionary conservation and specialization of cortico basal ganglia circuits in zebrafish	GSE254980	Other	The cortico basal ganglia circuit mediates decision making. Here we generated transgenic tools for adult zebrafish targeting specific subpopulations of the components of this circuit and utilized them to identify evolutionary homologs of the mammalian direct and indirect pathway striatal neurons which respectively project to the homologs of the internal and external segment of the globus pallidus dEN and Vl as in mammals. Unlike in mammals the Vl mainly projected to the dEN directly not by way of the subthalamic nucleus. Further single cell RNA sequencing analysis revealed two pallidal output pathways: a major shortcut pathway directly connecting the dEN with the pallium and the evolutionarily conserved closed loop by way of the thalamus. Our resources and circuit map provide the common basis for the functional study of the basal ganglia in a small and optically tractable zebrafish brain for the comprehensive mechanistic understanding of the cortico basal ganglia circuit. Overall design: To identify genetic markers of the npy negative thalamus projecting neurons in the dEN we conducted single cell RNA sequencing analysis. We dissected the dEN and its surrounding regions from six adult individuals of TgBACnpy:GAL4VP16;TgUAS:GFP. We then dissociated the dissected tissue and used the droplet based three primeend scRNAseq system Chromium 10x Genomics. We obtained transcriptomic data from 3 381 cells and performed unbiased clustering by Seurat.		pubmed:38484735		zebrafish dEN dissected tissue	GSM8061694		source name:dorsal entopeduncular nucleus and its surrounding brain tissue\|tissue:dorsal entopeduncular nucleus and its surrounding brain tissue\|cell type:Neurons/glia/blood cells from telencephalon\|genotype:TgBACnpy:GAL4VP16;TgUAS:GFP\|treatment:regular laboratory cultivation condition\|geo loc name:missing\|collection date:missing	zebrafish dEN dissected tissue	The obtained scRNAseq data of 3 381 cells were analyzed by Seurat.47 As a quality control cells with more than 6% mitochondrial genes less than 200 unique genes and more than 17500 UMIs were removed. Barcodes with less than 500 UMIs had been already removed by cellranger count pipeline. The remaining 3 043 cells were then data normalized by LogNormalize method with scale.factor = 10000. For further calculation of UMAP and clustering variable genes were determined with FindVariableFeatures function with selection.method = “vst” and the top 2000 most highly variable genes were used for further clustering. The expression of each gene was shifted so that the mean expression across cells is 0 and scaled so that the variance across cells is 1 by ScaleData function. PCA was run on the scaled data and then UMAP and clustering were performed with the FindNeighbors function with the top 35 PCs the FindClusters function with resolution = 0.5 and the RunUMAP function with the top 35 PCs. Dot plots and violin plots were generated by Seurat and cell types were determined by the expression of marker genes that define specific cell types. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Supplementary files format and content: HTML output file obtained from Seurat analysis using R markdown	dorsal entopeduncular nucleus and its surrounding brain tissue		Dissection was performed on 6 individuals of TgBACnpy:GAL4VP16;TgUAS:GFP fish and 12 dissected tissue pieces from the left and right hemispheres were obtained in total. The dEN and its surrounding regions were carefully dissected with micro scissors and fine forceps in ice cold and oxygenized Neurobasal medium ThermoFisher Scientific 21103049 supplemented with 1x B 27 ThermoFisher Scientific 17504044 under a fluorescent dissection microscope as shown in the Figure S5A. The dissected tissue was dissociated with the Papain Dissociation Kit Worthington; LK003150 with 0.1% 2 mercaptoethanol for 15 minutes with gentle shaking at 28.5 degrees Celsius. Then the cells were dissociated by gentle trituration 15 times with a glass Pasteur pipet coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The cells were resuspended in papain inhibitor solution Worthington and incubated for 10 minutes with gentle shaking at 28.5 degrees Celsius. Then the cells were further dissociated by gentle trituration 20 times with a glass Pasteur pipet attached with a regular 200 µl tip coated with 2% BSA in PBS. The dissociated cell suspension was then filtered with pluriStrainer Mini 40 µm pluriSelect coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The resulting cell suspension was resuspended in 2% BSA in PBS and then cell debris and dead cells were removed by FACS FACSAria SORP BD Biosciences using Hoechst to sort out cells from cell debris and Propidium Iodide to sort out living cells from dead cells. post FACS sorting a small fraction of the cell suspension was used to estimate the total number of the cells and their viability using a dead cell stain Trypan Blue elabscience. The obtained suspension contained 16 000 cells with 85.0% viability. The resulting single cell suspension was loaded on the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 10x Genomics PN 1000269 and the cDNA library was prepared according to the manufacturer’s instructions. The obtained cDNA library underwent Next generation sequencing by illumina Hiseq X GENEWIZ with 400 429 716 total reads and 85.9% of sequencing saturation. The obtained sequence was then analyzed by “Cell Ranger count” pipeline provided by 10x Genomics with default options. The reads were aligned to zebrafish reference transcriptome ENSEMBL Zv11 release 99 and EGFP CDS which were built by “Cell Ranger mkref” command based on zebrafish reference genome GRCz11 and annotation Ensembl 99. This resulted in 3 381 estimated number of cells with 4890 median unique molecular identifier UMI counts per cell.	regular laboratory cultivation condition	tissue:dorsal entopeduncular nucleus and its surrounding brain tissue\|cell type:Neurons/glia/blood cells from telencephalon\|genotype:TgBACnpy:GAL4VP16;TgUAS:GFP\|treatment:regular laboratory cultivation condition	GSM8061694	GSM8061694: zebrafish dEN dissected tissue; Danio rerio; RNA Seq	GSM8061694 r1	GSM8061694	1	Dissection was performed on 6 individuals of TgBACnpy:GAL4VP16;TgUAS:GFP fish and 12 dissected tissue pieces from the left and right hemispheres were obtained in total. The dEN and its surrounding regions were carefully dissected with micro scissors and fine forceps in ice cold and oxygenized Neurobasal medium ThermoFisher Scientific 21103049 supplemented with 1x B 27 ThermoFisher Scientific 17504044 under a fluorescent dissection microscope as shown in the Figure S5A. The dissected tissue was dissociated with the Papain Dissociation Kit Worthington; LK003150 with 0.1% 2 mercaptoethanol for 15 minutes with gentle shaking at 28.5 degrees Celsius. Then the cells were dissociated by gentle trituration 15 times with a glass Pasteur pipet coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The cells were resuspended in papain inhibitor solution Worthington and incubated for 10 minutes with gentle shaking at 28.5 degrees Celsius. Then the cells were further dissociated by gentle trituration 20 times with a glass Pasteur pipet attached with a regular 200 µl tip coated with 2% BSA in PBS. The dissociated cell suspension was then filtered with pluriStrainer Mini 40 µm pluriSelect coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The resulting cell suspension was resuspended in 2% BSA in PBS and then cell debris and dead cells were removed by FACS FACSAria SORP BD Biosciences using Hoechst to sort out cells from cell debris and Propidium Iodide to sort out living cells from dead cells. post FACS sorting a small fraction of the cell suspension was used to estimate the total number of the cells and their viability using a dead cell stain Trypan Blue elabscience. The obtained suspension contained 16 000 cells with 85.0% viability. The resulting single cell suspension was loaded on the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 10x Genomics PN 1000269 and the cDNA library was prepared according to the manufacturer's instructions. The obtained cDNA library underwent Next generation sequencing by illumina Hiseq X GENEWIZ with 400 429 716 total reads and 85.9% of sequencing saturation. The obtained sequence was then analyzed by “Cell Ranger count” pipeline provided by 10x Genomics with default options. The reads were aligned to zebrafish reference transcriptome ENSEMBL Zv11 release 99 and EGFP CDS which were built by “Cell Ranger mkref” command based on zebrafish reference genome GRCz11 and annotation Ensembl 99. This resulted in 3 381 estimated number of cells with 4890 median unique molecular identifier UMI counts per cell.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP487839		loader:fastq load.py	ENcDNALibrary20210701_S1_L002_I1_001.fastq.gz ENcDNALibrary20210701_S1_L002_I2_001.fastq.gz ENcDNALibrary20210701_S1_L002_R1_001.fastq.gz ENcDNALibrary20210701_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	53657581944.0	400429716.0	GSM8061694 r1	0:8 1:8 2:28 3:90	A:10793191703;C:7078696830;G:7719702279;T:10444591093;N:2492535	8	8	28	90	10793191703	7078696830	7719702279	10444591093	2492535	SRX23511536	SRS20362004	SRA1796958	CBS, RIKEN	CBS, RIKEN												B		usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Japan	2024-02-02	Undetermined	Adult	Brain	Nervous System