run_metadata: 66803
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 66803 | SRR16646359 | SRX12847065 | SRS10790601 | SRP343918 | PRJNA776627 | Enrichment and single cell sequencing of the ventricular cells from zebrafish telencephalon | GSE186874 | Other | Zebfrafish brains were injected with neutral cell tracking dye. Zebrafish telencephalon were dissociated and dye postive cells were sorted by FACS and single cell sequencing performed from these cells. Overall design: Zebrafish ventricular cells fom telencephalon were enriched by using cell tracking dye single cell sequencing of these cells was performed by 10X Genomics. | pubmed:35681503 | AS2 | GSM5662814 | tissue:telencephalon|tag:wilt type | AS2 | The fastq files were aligned to zebrafish transcript Ensembl Version 95by 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. Genome build: danRer11 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns. | telencephalon | Zebfrafish brains were injected with neutral cell tracking dye and 5 6 min post injection fish were sacrificed. | Cells from telencephalon were dissociated and cell tracking dye positve cells were sorted. The library preparation was performed by 10X Genomics as per manufactur protocol | Fish were kept at 28 °C water system with 14/10 hours light/dark cycles | tag:wilt type | GSM5662814 | GSM5662814: AS2; Danio rerio; RNA Seq | GSM5662814 | 1 | Cells from telencephalon were dissociated and cell tracking dye positve cells were sorted. The library preparation was performed by 10X Genomics as per manufactur protocol | GEO Accession:GSM5662814 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP343918 | assembly:danRer11|intentional duplicate | WTAB_12M_possorted_genome_bam.bam | 10X Genomics bam file | 9121417308.0 | 98079756.0 | GSM5662814 r1 | 0:93 | A:2807824317;C:1747195814;G:1887252370;T:2679004798;N:140009 | 93 | 2807824317 | 1747195814 | 1887252370 | 2679004798 | 140009 | SRX12847065 | SRS10790601 | SRA1320126 | GEO | AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association | 1 | 0.88535 | 0.29534 | 0.73933 | 0.50975 | 93 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-10-31 | Undetermined | Undetermined | Brain | Nervous System |