run_metadata: 69108
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 69108 | SRR19574840 | SRX14566116 | SRS12343114 | SRP363983 | PRJNA816047 | Mapping the zebrafish developmental and aging atlas by single cell mRNA seq | GSE198571 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA817101 | pubmed:35929025 | Micorwell seq datasets of Zebrafish 22m COL98 | GSM5965369 | source name:Zebrafish 22m sample1|strain:AB|age:22 month|tissue:whole organism | Micorwell seq datasets of Zebrafish 22m COL98 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 22m sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:22 month|tissue:whole organism | GSM5965369 | GSM5965369: Micorwell seq datasets of Zebrafish 22m COL98; Danio rerio; RNA Seq | GSM5965369 r1 | GSM5965369 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | DNBSEQ | DNBSEQ-T7 | SRP363983 | Zebrafish_22m_COL98_2_2.fq.gz Zebrafish_22m_COL98_2_1.fq.gz | fastq fastq | 18950667342.0 | 146904398.0 | GSM5965369 r2 | 0:108 1:150 | A:5563615657;C:3754580615;G:4025718357;T:5579503919;N:27248794 | 108 | 150 | 5563615657 | 3754580615 | 4025718357 | 5579503919 | 27248794 | SRX14566116 | SRS12343114 | SRA1461257 | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.38541 | 0.02055 | 0.91595 | 0.44038 | 108 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2022-03-22 | Adult | Adult | Whole Organism | All anatomical structures |