{"database": "metadata", "table": "run_metadata", "rows": [[34551, "SRR32104356", "SRX27449954", "SRS23876475", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Positive CNC 3", "GSM8751787", null, "source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing", "17hpf Positive CNC 3", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "cardiac neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +", "GSM8751787", "GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq", "GSM8751787 r1", "GSM8751787", "1", "mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz", "fastq", 5836253400.0, 58362534.0, "GSM8751787 r1", "0:100", "A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036", 100, null, null, null, 1666874971, 1250406201, 1263794016, 1655113176, 65036, "SRX27449954", "SRS23876475", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Multi-tissue", "Multi-system"]], "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": ["34551"], "units": {}, "query_ms": 10.63645799877122}