run_metadata: 34325

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
34325	SRR31647631	SRX27010713	SRS23475006	SRP550229	PRJNA1195876	Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq]	GSE283840	Transcriptome Analysis	Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically Amh binds to its receptors Bmpr2a/Bmpr1bb which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.		pubmed:40348785		pituitary gland WT	GSM8672963		source name:pituitary gland\|tissue:pituitary gland\|genotype:WT\|geo loc name:missing\|collection date:missing	pituitary gland WT	Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	pituitary gland		post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer’s solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.		tissue:pituitary gland\|genotype:WT	GSM8672963	GSM8672963: pituitary gland WT; Danio rerio; RNA Seq	GSM8672963 r1	GSM8672963	1	post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer's solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP550229			WT_R1.fq.gz WT_R2.fq.gz	fastq fastq	149500940700.0	498336469.0	GSM8672963 r1	0:150 1:150	A:49714239420;C:27445649314;G:26079818385;T:46259970208;N:1263373	150	150			49714239420	27445649314	26079818385	46259970208	1263373	SRX27010713	SRS23475006	SRA2029986	Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences	Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences												T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2024-12-09	Undetermined	Undetermined	Pituitary Gland	Endocrine System