run_metadata: 63469
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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| 63469 | SRR13839971 | SRX10218347 | SRS8362930 | SRP309047 | PRJNA706197 | scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish | GSE168133 | Transcriptome Analysis | We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration. | parent bioproject:PRJNA706402 | pubmed:34936864 | FACS sorted NC cells 24 hpf | GSM5129557 | tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell | FACS sorted NC cells 24 hpf | FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv barcode.1 corresponds to "Sample 1" barcode.2 corresponds to "Sample 2" and so on. | FACS sorted sox10:nEOS cells | Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 | genotype:Tgsox10:nEOSw18|age:24 hpf|cell type:NC cell | GSM5129557 | GSM5129557: FACS sorted NC cells 24 hpf; Danio rerio; RNA Seq | GSM5129557 | 1 | Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 | GEO Accession:GSM5129557 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP309047 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=Arch 1 24hpf S7 L001 I1 001.fastq.gz read2PairFiles=Arch 1 24hpf S7 L001 R1 001.fastq.gz read3PairFiles=Arch 1 24hpf S7 L001 R2 001.fastq.gz | Arch_1_24hpf_S7_L001_I1_001.fastq.gz Arch_1_24hpf_S7_L001_R1_001.fastq.gz Arch_1_24hpf_S7_L001_R2_001.fastq.gz | fastq fastq fastq | 3530802792.0 | 26748506.0 | GSM5129557 r3 | 0:8 1:26 2:98 | A:953651270;C:750587344;G:854819839;T:970588117;N:1156222 | 8 | 26 | 98 | 953651270 | 750587344 | 854819839 | 970588117 | 1156222 | SRX10218347 | SRS8362930 | SRA1202350 | GEO | Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine | 1 | 0.93059 | 0.08636 | 0.81927 | 0.52426 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-03-03 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |