{"database": "metadata", "table": "run_metadata", "rows": [[74319, "SRR23635454", "SRX19518496", "SRS16905858", "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 \u201creader\u201d  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", null, "KO  replicate 1  scRNAseq", "GSM7067527", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  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", null, "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 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  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\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067527", "GSM7067527: KO  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067527 r1", "GSM7067527", "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 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO1_S1_L003_R1_001.fastq.gz KO1_S1_L003_R2_001.fastq.gz", "fastq fastq", 49793178900.0, 165977263.0, "GSM7067527 r3", "0:150 1:150", "A:15157773060;C:7439911776;G:8061299298;T:19134016399;N:178367", 150, 150, null, null, 15157773060, 7439911776, 8061299298, 19134016399, 178367, "SRX19518496", "SRS16905858", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.29177, 0.91563, 0.11066, 0.20906, 0.97155, 0.77068, 0.52121, 0.5115, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["74319"], "units": {}, "query_ms": 13.590483998996206}