run_metadata: 74325

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
74325	SRR23635460	SRX19518494	SRS16905857	SRP425043	PRJNA939369	The TET BMP regulatory axis in pathogenesis of CFM [scRNA]	GSE226183	Transcriptome Analysis	Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.	parent bioproject:PRJNA939357	pubmed:38427557		WT replicate 1 scRNAseq	GSM7067525		source name:embryo\|tissue:embryo\|age:48 hpf\|genotype:wild type\|geo loc name:missing\|collection date:missing	WT replicate 1 scRNAseq	The demultiplexing barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files	embryo		The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma D4818 and incubated at 0.5U 33 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer’s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.		tissue:embryo\|age:48 hpf\|genotype:wild type	GSM7067525	GSM7067525: WT replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM7067525 r1	GSM7067525	1	The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma D4818 and incubated at 0.5U 33 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP425043			WT1_S1_L001_R1_001.fastq.gz WT1_S1_L001_R2_001.fastq.gz	fastq fastq	65856223500.0	219520745.0	GSM7067525 r1	0:150 1:150	A:21355018202;C:9465269057;G:9803481122;T:25230563681;N:1891438	150	150			21355018202	9465269057	9803481122	25230563681	1891438	SRX19518494	SRS16905857	SRA1597330	Yunnan University	Yunnan University	2	0.32204	0.8947	0.14108	0.2604	0.96495	0.75566	0.5149	0.51562	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures