{"database": "metadata", "table": "run_metadata", "rows": [[32098, "SRR29008446", "SRX24535482", "SRS21281082", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Chondrocyte head biolRep3", "GSM8264152", null, "source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Chondrocyte head biolRep3", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264152", "GSM8264152: Chondrocyte head biolRep3; Danio rerio; RNA Seq", "GSM8264152 r1", "GSM8264152", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "cartilRep3_R1.fastq.gz cartilRep3_R2.fastq.gz", "fastq fastq", 6819648393.0, 25781563.0, "GSM8264152 r1", "0:132.28 1:132.24", "A:1843991471;C:1548648708;G:1568393744;T:1858508350;N:106120", 132, 132, null, null, 1843991471, 1548648708, 1568393744, 1858508350, 106120, "SRX24535482", "SRS21281082", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous 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": ["32098"], "units": {}, "query_ms": 9.971032000976265}