run_metadata: 35979
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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| 35979 | SRR33380663 | SRX28623695 | SRS24895016 | SRP582260 | PRJNA1256738 | Angptl5 restricts primitive hematopoiesis by modulating retinoic acid signaling in zebrafish | GSE295891 | Other | Purpose: Characterization of cell types in angptl5?10/?10 zebrafish. Methods: The angptl5?10/?10 embryos were raised in 0.3× Danieau Buffer and harvested at 16 hpf. Collected samples were digested with trypsin into single cell suspension for single cell sequencing. Libraries were constructed with a Chromium Single Cell three primev3 Reagent Kit 10x Genomics according to the manufacturer's protocol for 7350 cell recovery.Sequencing was performed with Illumina Novaseq 6000 according to the manufacturer's instructions Illumina. Results: Global amplification of myeloid and erythroid progenitors in angptl5?10/?10 embryos. Conclusions: Angptl5 regulated primitive hematopoiesis in zebrafish. Overall design: Collected samples of angptl5?10/?10 embryos at 16 hpf were digested with trypsin into single cell suspension for scRNA seq. | A5 / 16 hpf | GSM8960245 | source name:embryonic cells|tissue:embryonic cells|strain:AB|cell type:embryonic cells|genotype:angptl5 mutant|treatment:CRISPR/Cas9 knockout|batch:A5 16h|geo loc name:missing|collection date:missing | A5 / 16 hpf | Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar compressed files include filtered gene bc matrices post running CellRanger pipeline | embryonic cells | Collected samples were digested with trypsin into single cell suspension and set to Novogene for single cell sequencing. | RNA from the barcoded cells was reverse transcribed reagents from a Chromium Single Cell reagent kit 10X Genomics Libraries were prepared using Single Cell 3′Library & gel Bead kit v3 10x Genomics Cat# PN 1000268 according to the manufacturer’s protocol for 7350 cell recovery. | The angptl5Δ10/Δ10 embryos were raised in 0.3× Danieau Buffer and harvested at 16 hpf | tissue:embryonic cells|strain:AB|cell type:embryonic cells|genotype:angptl5 mutant|treatment:CRISPR/Cas9 knockout|batch:A5 16h | GSM8960245 | GSM8960245: A5 / 16 hpf; Danio rerio; RNA Seq | GSM8960245 r1 | GSM8960245 | 1 | RNA from the barcoded cells was reverse transcribed reagents from a Chromium Single Cell reagent kit 10X Genomics Libraries were prepared using Single Cell 3′Library & gel Bead kit v3 10x Genomics Cat# PN 1000268 according to the manufacturer's protocol for 7350 cell recovery. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP582260 | A5_16h-zebra_S1_L001_R1_001.fastq.gz A5_16h-zebra_S1_L001_R2_001.fastq.gz | fastq fastq | 126632686800.0 | 422108956.0 | GSM8960245 r1 | 0:150 1:150 | A:31741347954;C:28608734203;G:22541136036;T:43733881512;N:7587095 | 150 | 150 | 31741347954 | 28608734203 | 22541136036 | 43733881512 | 7587095 | SRX28623695 | SRS24895016 | SRA2121245 | Institute of genetics, Zhejiang University | Institute of genetics, Zhejiang University | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2025-04-29 | Segmentation | Embryo | Embryo Imprecise | All anatomical structures |