run_metadata
2 rows where experiment.platform = "ILLUMINA", technology = "microwellseq" and tissue_curation = "Whole Organism"
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| Link | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 64962 | 64962 | SRR15293962 | SRX11598734 | SRS9635704 | 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 | Micorwell seq datasets of Zebrafish 24h COL2 | GSM5484286 | source name:Zebrafish 24h COL|strain:AB|age:24 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 24h COL2 | 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 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. 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 24h COL | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5484286 | GSM5484286: Micorwell seq datasets of Zebrafish 24h COL2; Danio rerio; RNA Seq | GSM5484286 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | GEO Accession:GSM5484286 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24h_COL2.bam | bam | 30695841720.0 | 101641860.0 | GSM5484286 r1 | 0:151 1:151 | A:8070725571;C:5211775632;G:5264888732;T:12140996276;N:7455509 | 151 | 151 | 8070725571 | 5211775632 | 5264888732 | 12140996276 | 7455509 | SRX11598734 | SRS9635704 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 2e-05 | 0.70367 | 0.0 | 0.01973 | 0.99997 | 0.84756 | 1.0 | 0.49242 | 151 | 151 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-07-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures | ||||||||||
| 64963 | 64963 | SRR15293961 | SRX11598733 | SRS9635703 | 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 | Micorwell seq datasets of Zebrafish 24h COL1 | GSM5484285 | source name:Zebrafish 24h COL|strain:AB|age:24 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 24h COL1 | 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 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. 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 24h COL | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5484285 | GSM5484285: Micorwell seq datasets of Zebrafish 24h COL1; Danio rerio; RNA Seq | GSM5484285 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | GEO Accession:GSM5484285 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24h_COL1.bam | bam | 36227583572.0 | 119958886.0 | GSM5484285 r1 | 0:151 1:151 | A:9526054168;C:6077203407;G:6186063574;T:14428929871;N:9332552 | 151 | 151 | 9526054168 | 6077203407 | 6186063574 | 14428929871 | 9332552 | SRX11598733 | SRS9635703 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.0 | 0.68952 | 0.0 | 0.01903 | 1.0 | 0.85167 | 0.4788 | 151 | 151 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-07-29 | Pharyngula | Embryo | Whole Organism | All anatomical structures |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;