run_metadata: 68520
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 68520 | SRR17900894 | SRX14059604 | SRS11892524 | SRP358576 | PRJNA803902 | High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration | GSE196211 | Transcriptome Analysis | NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr | pubmed:35316618 | 30min post neomycin | GSM5862801 | source name:neuromast|age:5dpf|tissue:neuromast|treatment/time point:30min post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP | 30min post neomycin | Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell. | neuromast | Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq | age:5dpf|tissue:neuromast|treatment/time point:30min post neomycin|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP | GSM5862801 | GSM5862801: 30min post neomycin; Danio rerio; RNA Seq | GSM5862801 r1 | GSM5862801 | 1 | Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP358576 | assembly:danRer10|intentional duplicate | 30min_possorted_genome_bam.bam | 10X Genomics bam file | 15228653913.0 | 153824787.0 | GSM5862801 r1 | 0:99 | A:4774203586;C:3007224980;G:3233337864;T:4213847766;N:39717 | 99 | 4774203586 | 3007224980 | 3233337864 | 4213847766 | 39717 | SRX14059604 | SRS11892524 | SRA1367859 | Piotrowski Lab, Stowers Institute for Medical Research | Piotrowski Lab, Stowers Institute for Medical Research | 1 | 0.92255 | 0.24454 | 0.83128 | 0.55089 | 99 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-02-06 | Larval | Larval | Lateral Line | Sensory System |