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
74329,SRR23635030,SRX19518333,SRS16905710,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,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: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,KO  replicate 2  bulk RNAseq,GSM7067524,,source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing,KO  replicate 2  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out,GSM7067524,GSM7067524: KO  replicate 2  bulk RNAseq; Danio rerio; RNA Seq,GSM7067524 r1,GSM7067524,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,KO2.fastq.gz,fastq,4188284200.0,41882842.0,GSM7067524 r1,0:100,A:1066992737;C:1011357361;G:1055554148;T:1041284278;N:13095676,100,,,,1066992737,1011357361,1055554148,1041284278,13095676,SRX19518333,SRS16905710,SRA1597336,Yunnan University,Yunnan University,1,0.88647,,0.07541,,0.7237,,0.47069,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
74330,SRR23635031,SRX19518332,SRS16905709,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,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: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,KO  replicate 1  bulk RNAseq,GSM7067523,,source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing,KO  replicate 1  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out,GSM7067523,GSM7067523: KO  replicate 1  bulk RNAseq; Danio rerio; RNA Seq,GSM7067523 r1,GSM7067523,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,KO1.fastq.gz,fastq,4181083400.0,41810834.0,GSM7067523 r1,0:100,A:1077414361;C:996554293;G:1053357384;T:1040649776;N:13107586,100,,,,1077414361,996554293,1053357384,1040649776,13107586,SRX19518332,SRS16905709,SRA1597336,Yunnan University,Yunnan University,1,0.87685,,0.07522,,0.72699,,0.48859,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
74331,SRR23635032,SRX19518331,SRS16905708,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,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: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,WT  replicate 2  bulk RNAseq,GSM7067522,,source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing,WT  replicate 2  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:wild type,GSM7067522,GSM7067522: WT  replicate 2  bulk RNAseq; Danio rerio; RNA Seq,GSM7067522 r1,GSM7067522,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,WT2.fastq.gz,fastq,1435167700.0,14351677.0,GSM7067522 r1,0:100,A:371412640;C:334204906;G:351277070;T:371684263;N:6588821,100,,,,371412640,334204906,351277070,371684263,6588821,SRX19518331,SRS16905708,SRA1597336,Yunnan University,Yunnan University,1,0.83841,,0.15087,,0.71417,,0.50982,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
74332,SRR23635033,SRX19518330,SRS16905707,SRP425040,PRJNA939370,The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq],GSE226182,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: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.,parent bioproject:PRJNA939357,pubmed:38427557,,WT  replicate 1  bulk RNAseq,GSM7067521,,source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing,WT  replicate 1  bulk RNAseq,Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample,embryo,,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,tissue:embryo|age:48 hpf|genotype:wild type,GSM7067521,GSM7067521: WT  replicate 1  bulk RNAseq; Danio rerio; RNA Seq,GSM7067521 r1,GSM7067521,1,RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,DNBSEQ,DNBSEQ-G400,,SRP425040,,,WT1.fastq.gz,fastq,1961618800.0,19616188.0,GSM7067521 r1,0:100,A:518460045;C:447438337;G:477081234;T:509513188;N:9125996,100,,,,518460045,447438337,477081234,509513188,9125996,SRX19518330,SRS16905707,SRA1597336,Yunnan University,Yunnan University,1,0.81315,,0.14097,,0.72342,,0.50905,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2023-02-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures