run_metadata: 54432
This data as json
| 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 |
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| 54432 | SRR10126276 | SRX6854673 | SRS5392875 | 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 | pubmed:31908317 | RG 4 02 G10 | GSM4081162 | tissue:Brain|sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.622636514669279 | RG 4 02 G10 | 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: ‘gsnap.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’ 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 | 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. | sorting:RG|FISH id:bfx855 02|batch:bfx855|fraction mapped:0.622636514669279 | GSM4081162 | GSM4081162: RG 4 02 G10; Danio rerio; RNA Seq | GSM4081162 | 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:GSM4081162 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP221784 | intentional duplicate|dangling references:treat as unmapped | L24001_RG_4_02_G10_mod.bam | bam | 24974740.0 | 328615.0 | GSM4081162 r1 | 0:76 | A:7027112;C:5576222;G:5635470;T:6735797;N:139 | 76 | 7027112 | 5576222 | 5635470 | 6735797 | 139 | SRX6854673 | SRS5392875 | SRA962624 | GEO | Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems | 1 | 0.84236 | 0.05961 | 0.98472 | 0.57975 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | nextera | sc_generic | single_cell_generic | generic-scrnaseq-only | Germany | 2019-09-16 | Adult | Adult | Brain | Nervous System |