run_metadata: 33295

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
33295	SRR29920544	SRX25414718	SRS22075126	SRP521426	PRJNA1138768	Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics	GSE272806	Transcriptome Analysis	Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish however is an exception as gnrh3–/– fish which lack the hypophysiotropic GnRH3 are fertile suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2 thyroid hormone estrogen dopamine and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes instead the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2 but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression probably via a non Gnrh receptor route. Altogether while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing		pubmed:39499852		WT scRNAseq	GSM8412847		source name:Pituitary\|tissue:Pituitary\|age:Adult 3 mpf\|genotype:wild type\|Sex:female\|geo loc name:missing\|collection date:missing	WT scRNAseq	Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control normalization data integration and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files matrix file and comma separated values file	Pituitary		Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample.		tissue:Pituitary\|age:Adult 3 mpf\|genotype:wild type\|Sex:female	GSM8412847	GSM8412847: WT scRNAseq; Danio rerio; RNA Seq	GSM8412847 r1	GSM8412847	1	Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP521426		loader:fastq load.py	WT_20210616_A00904_IL100185603_S1_L001_I1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_I2_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	26784946020.0	120652910.0	GSM8412847 r1	0:10 1:10 2:101 3:101	A:6396247260;C:3989076165;G:4295547390;T:9690479627;N:537378	10	10	101	101	6396247260	3989076165	4295547390	9690479627	537378	SRX25414718	SRS22075126	SRA1930291	Stanford University	Stanford University	2	0.10896	0.92399	0.02311	0.16455	0.97652	0.80377	0.67721	0.64804	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2024-07-22	Adult	Adult	Pituitary Gland	Endocrine System