run_metadata: 74458
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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| 74458 | SRR23802705 | SRX19634573 | SRS17003744 | SRP426627 | PRJNA943249 | Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche] | GSE227117 | Transcriptome Analysis | We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized filtered and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. | parent bioproject:PRJNA510836 | kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2 | GSM7091919 | source name:kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type|tissue:embryos|genotype:wild type | kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2 | the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode | kdrl:GFP mrc1a.125:GFP transgenic zebrafish embryos wild type | No treatments | Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells. | tissue:embryos|genotype:wild type | GSM7091919 | GSM7091919: kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2; Danio rerio; RNA Seq | GSM7091919 r1 | GSM7091919 | 1 | Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP426627 | GR4_Single_Cell_TCTTACGC.fastq.sorted.fastq.gz | fastq | 13661225700.0 | 102550405.0 | GSM7091919 r1 | 0:133.21 | A:4263167363;C:2771561232;G:2605236063;T:4020689114;N:571928 | 133 | 4263167363 | 2771561232 | 2605236063 | 4020689114 | 571928 | SRX19634573 | SRS17003744 | Oncology/Hematology, Boston Children's Hospital | 1 | 0.64929 | 0.08349 | 0.80462 | 0.50638 | 149 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | indrops | United States | 2023-03-10 | Larval | Larval | Embryo Imprecise | All anatomical structures |