run_metadata: 30017
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30017 | SRR28164891 | SRX23795137 | SRS20618181 | SRP485064 | PRJNA1067370 | zebrafish embryo for scRNA seq and bulk RNA seq | PRJNA1067370 | Other | Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis. | 10x Genomics multiplexing GEX | scRNA seq wild type and hamp / 12 hpf GEX | Zebrafish embryo scRNA seq wild type and hamp / 12 hpf GEX | strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf GEX|dev stage:12 hpf GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal | scRNA seq wild type and hamp / 12 hpf GEX | G 1 | G 1 | 10x Genomics multiplexing GEX | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP485064 | 12h_Gene_Expression_S1_L001_R2_001.fastq.gz 12h_Gene_Expression_S1_L001_R1_001.fastq.gz | fastq fastq | 204426398700.0 | 681421329.0 | 12h Gene Expression S1 L001 R1 001.fastq.gz | 0:150 1:150 | A:61302872939;C:35072603645;G:37153666376;T:70891933893;N:5321847 | 150 | 150 | 61302872939 | 35072603645 | 37153666376 | 70891933893 | 5321847 | SRX23795137 | SRS20618181 | SRA1813495 | Shanghai Ocean University|College of Fisheries and Life | Shanghai Ocean University | 2 | 0.00085 | 0.9058 | 0.0 | 0.12081 | 0.99991 | 0.80231 | 0.5 | 0.52456 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2024-02-29 | Segmentation | Embryo | Embryo Imprecise | All anatomical structures |