{"database": "metadata", "table": "run_metadata", "rows": [[74201, "SRR23592283", "SRX19477370", "SRS16868713", "SRP424004", "PRJNA937732", "Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution", "GSE225863", "Transcriptome Analysis", "The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia  also called macroglia  make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing  maintaining and assiting neurons. Despite their importance  glial cells have been much less studied than neurons. Here  in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support  we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.", null, "pubmed:38518783", null, "Replicate1", "GSM7058864", null, "source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "Replicate1", "The demultiplexing  barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Telencephalon", null, "Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks", "GSM7058864", "GSM7058864: Replicate1; Danio rerio; RNA Seq", "GSM7058864 r1", "GSM7058864", "1", "Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP424004", null, "loader:fastq load.py", "Replicate1_S2_L002_I1_001.fastq.gz Replicate1_S2_L002_R1_001.fastq.gz Replicate1_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 11111432772.0, 84177521.0, "GSM7058864 r1", "0:8 1:26 2:98", "A:2488056016;C:1560451855;G:1702518729;T:2495889662;N:2480796", 8, 26, 98, null, 2488056016, 1560451855, 1702518729, 2495889662, 2480796, "SRX19477370", "SRS16868713", "SRA1594515", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", "Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur", 1, 0.86994, null, 0.32454, null, 0.75479, null, 0.50147, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2023-02-22", "Juvenile", "Juvenile", "Brain", "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": ["74201"], "units": {}, "query_ms": 12.792403998901136}