run_metadata: 64557
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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| 64557 | SRR14915013 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | 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 5 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 6 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. Genome build: 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 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_2_1.fq.gz Zebrafish_3m_COL61_2_2.fq.gz | fastq fastq | 1240206900.0 | 8268046.0 | GSM5400022 r2 | 0:150 1:150 | A:342697940;C:238587916;G:245987086;T:412298823;N:635135 | 150 | 150 | 342697940 | 238587916 | 245987086 | 412298823 | 635135 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13399 | 0.008 | 0.9181 | 0.52385 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures |