{"database": "metadata", "table": "run_metadata", "rows": [[28752, "SRR26623289", "SRX22323899", "SRS19374429", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Brain 9   telencephalon  scRNAseq", "GSM7875168", null, "source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Brain 9   telencephalon  scRNAseq", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875168", "GSM7875168: Brain 9   telencephalon  scRNAseq; Danio rerio; RNA Seq", "GSM7875168 r1", "GSM7875168", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP469552", null, "loader:fastq load.py", "b9_tel_R1.fastq.gz b9_tel_R2.fastq.gz", "fastq fastq", 15193441000.0, 122527750.0, "GSM7875168 r1", "0:26 1:98", "A:4477414579;C:3090884741;G:3307200604;T:4310709839;N:7231237", 26, 98, null, null, 4477414579, 3090884741, 3307200604, 4310709839, 7231237, "SRX22323899", "SRS19374429", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00277, 0.88718, 0.00117, 0.25579, 0.99586, 0.79657, 0.30868, 0.52408, 26, 98, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "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": ["28752"], "units": {}, "query_ms": 11.609709999902407}