{"database": "metadata", "table": "run_metadata", "rows": [[74359, "SRR23690177", "SRX19552674", "SRS16937432", "SRP425371", "PRJNA940435", "sox1a:eGFP transgenic line and single cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons", "GSE226494", "Transcriptome Analysis", "The Sox family of transcription factors plays a crucial role in the development of the vertebrate nervous system. In the zebrafish embryo  sox1 genes are expressed in neural progenitor cells and neurons of the ventral spinal cord. We recently reported that the loss of function of sox1a and sox1b results in a significant decrease in a subtype of V2 neurons  called V2s  in zebrafish. Here a single cell RNA sequencing scRNA Seq approach was used to analyse the transcriptome of sox1a lineage progenitors and neurons in the zebrafish spinal cord at four different time points during the development of an earlier established Tgsox1a:EGFP line. In addition to the sox1a expressing neurons described previously  we found that this gene is also expressed in late developing intraspinal serotonin neurons ISNs. Developmental trajectory analysis of single cell data and morpholino knockdown of lateral floor plate LFP cells expressing the nkx2.9 gene suggest that ISNs are generated from LFP progenitor cells. Pharmacological inhibition of the Notch signalling pathway demonstrates the necessity of this pathway for the development of LFP progenitor cells into ISN populations. Our results confirm that the zebrafish LFP is a progenitor domain from which ISN neurons are generated in addition to the previously described KA\" and V3. Overall design: The trunk and tail of Tgsox1a:eGFP lines were and dissected at 1  2 dpf 3 dpf and 5 dpf. The tissue  was dissociated and GFP positive cells were sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation  cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit  and Sequencing done by Illumina.", null, "pubmed:37529101", null, "sox1a 2dpf", "GSM7077908", null, "source name:spinal cord|tissue:spinal cord|genotype:Tgsox1a:eGFP|time point:2dpf|geo loc name:missing|collection date:missing", "sox1a 2dpf", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 104 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger", "spinal cord", "No treatment done.", "Cells from zebrafish spinla cord were dissociated  and sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", "Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH\u00a07.5  at 28\u00a0\u00b0C \u00b11\u00a0\u00b0C in groups of 20 animals per 2.8\u00a0L.\u00a0", "tissue:spinal cord|genotype:Tgsox1a:eGFP|time point:2dpf", "GSM7077908", "GSM7077908: sox1a 2dpf; Danio rerio; RNA Seq", "GSM7077908 r1", "GSM7077908", "1", "Cells from zebrafish spinla cord were dissociated  and sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP425371", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped", "2dpf_possorted_genome_bam.bam", "10X Genomics bam file", 6112999144.0, 60524744.0, "GSM7077908 r1", "0:101", "A:1707014148;C:1361654515;G:1549767034;T:1494373967;N:189480", 101, null, null, null, 1707014148, 1361654515, 1549767034, 1494373967, 189480, "SRX19552674", "SRS16937432", "SRA1601794", "Rastegar, Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT)", "Rastegar, Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT)", 1, 0.90304, null, 0.26514, null, 0.79117, null, 0.59637, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-03-02", "Hatching", "Embryo", "Spinal Cord", "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": ["74359"], "units": {}, "query_ms": 10.743985010776669}