{"database": "metadata", "table": "run_metadata", "rows": [[54378, "SRR10126150", "SRX6854727", "SRS5392929", "SRP221784", "PRJNA565778", "Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain", "GSE137525", "Transcriptome Analysis", "Zebrafish display widespread and pronounced adult neurogenesis  which is fundamental for their regeneration capability post central nervous system injury. However  the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here  we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia  newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically  we detected 2 separate newborn neuron types  which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain  identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus  we prospectively isolated adult newborn neurons from the adult zebrafish forebrain  identified markers for newborn and mature neurons in the adult brain  revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain", null, "pubmed:31908317", null, "NBN 1 01 A07", "GSM4081036", null, "tissue:Brain|sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.51658557940085", "NBN 1 01 A07", "FastQC was used to   examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: \u2018gsnap.sse42  D /projects/seq work/user/pipeline/gmap  d GRCz10   gunzip  A sam  t 14   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 87.ss.GRCz10.iit   read group id=L22281 ON15 01 G10   read group name=ON15 01 G10   read group library=L22281   read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz\u2019 Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: \" a\" \"/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf\" \" s\" \"2\" \" o\" \"genecount/bfx811.GRCz10.e87.txt\" \" Q\" \"1\" \" T\" \"8\" \"  tmpDir\" \"/tmp/418815.1.ngs.q\" Genome build: GRCz10 reference  inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.", "Brain", null, "adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.", null, "sorting:NBN|FISH id:bfx855 01|batch:bfx855|fraction mapped:0.51658557940085", "GSM4081036", "GSM4081036: NBN 1 01 A07; Danio rerio; RNA Seq", "GSM4081036", null, "1", "adult zebrafish brains were collected  digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.", "GEO Accession:GSM4081036", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP221784", null, "intentional duplicate|dangling references:treat as unmapped", "L23875_NBN_1_01_A07_mod.bam", "bam", 30545692.0, 401917.0, "GSM4081036 r1", "0:76", "A:8429583;C:6966930;G:7076371;T:8072681;N:127", 76, null, null, null, 8429583, 6966930, 7076371, 8072681, 127, "SRX6854727", "SRS5392929", "SRA962624", "GEO", "Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems", 1, 0.79087, null, 0.10941, null, 0.9656, null, 0.51011, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2019-09-16", "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": ["54378"], "units": {}, "query_ms": 13.120653995429166}