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
64506,SRR17299063,SRX13476323,SRS11373166,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 24hpf COL58,GSM5746868,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL58,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746868,GSM5746868: Microwell seq datasets of Zebrafish 24hpf COL58; Danio rerio; RNA Seq,GSM5746868,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL58.bam,bam,91823975304.0,527723996.0,GSM5746868 r1,0:24 1:150,A:27162173122;C:19911517883;G:21018214314;T:23663599459;N:68470526,24,150,,,27162173122,19911517883,21018214314,23663599459,68470526,SRX13476323,SRS11373166,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00273,0.74807,0.00242,0.067,0.99949,0.84889,0.32,0.62031,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64507,SRR17299062,SRX13476322,SRS11373165,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 24hpf COL57,GSM5746867,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL57,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746867,GSM5746867: Microwell seq datasets of Zebrafish 24hpf COL57; Danio rerio; RNA Seq,GSM5746867,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL57.bam,bam,83668974276.0,480856174.0,GSM5746867 r1,0:24 1:150,A:24589284117;C:18203396283;G:19071978317;T:21739883658;N:64431901,24,150,,,24589284117,18203396283,19071978317,21739883658,64431901,SRX13476322,SRS11373165,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00288,0.75168,0.00269,0.07335,0.99969,0.84419,0.6,0.6312,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64508,SRR17299061,SRX13476321,SRS11373164,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 24hpf COL56,GSM5746866,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL56,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746866,GSM5746866: Microwell seq datasets of Zebrafish 24hpf COL56; Danio rerio; RNA Seq,GSM5746866,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL56.bam,bam,86257073418.0,495730307.0,GSM5746866 r1,0:24 1:150,A:25447223471;C:18668491192;G:19647110520;T:22426583347;N:67664888,24,150,,,25447223471,18668491192,19647110520,22426583347,67664888,SRX13476321,SRS11373164,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00275,0.73434,0.00255,0.07548,0.99967,0.84325,0.4375,0.5398,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64509,SRR17299060,SRX13476320,SRS11373163,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 24hpf COL55,GSM5746865,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL55,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746865,GSM5746865: Microwell seq datasets of Zebrafish 24hpf COL55; Danio rerio; RNA Seq,GSM5746865,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL55.bam,bam,90331122120.0,519144380.0,GSM5746865 r1,0:24 1:150,A:26895594483;C:19418243460;G:20453276913;T:23498626121;N:65381143,24,150,,,26895594483,19418243460,20453276913,23498626121,65381143,SRX13476320,SRS11373163,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00295,0.73613,0.00277,0.07262,0.99971,0.83926,0.66666,0.56101,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64510,SRR17299059,SRX13476319,SRS11373162,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 24hpf COL53,GSM5746864,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL53,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746864,GSM5746864: Microwell seq datasets of Zebrafish 24hpf COL53; Danio rerio; RNA Seq,GSM5746864,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL53.bam,bam,89040837126.0,511728949.0,GSM5746864 r1,0:24 1:150,A:26403646377;C:19129690981;G:20273444200;T:23171059435;N:62996133,24,150,,,26403646377,19129690981,20273444200,23171059435,62996133,SRX13476319,SRS11373162,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00256,0.73401,0.00242,0.07541,0.99977,0.83731,0.36363,0.56119,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64511,SRR17299058,SRX13476318,SRS11373161,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 24hpf COL52,GSM5746863,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL52,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746863,GSM5746863: Microwell seq datasets of Zebrafish 24hpf COL52; Danio rerio; RNA Seq,GSM5746863,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL52.bam,bam,92071528062.0,529146713.0,GSM5746863 r1,0:24 1:150,A:27250499787;C:19863195558;G:21006813218;T:23884436340;N:66583159,24,150,,,27250499787,19863195558,21006813218,23884436340,66583159,SRX13476318,SRS11373161,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00303,0.73044,0.00285,0.07319,0.99969,0.84118,0.6,0.55998,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64512,SRR17299057,SRX13476317,SRS11373160,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 24hpf COL51,GSM5746862,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL51,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746862,GSM5746862: Microwell seq datasets of Zebrafish 24hpf COL51; Danio rerio; RNA Seq,GSM5746862,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL51.bam,bam,89393336592.0,513754808.0,GSM5746862 r1,0:24 1:150,A:26357157407;C:19229237017;G:20353675917;T:23391840285;N:61425966,24,150,,,26357157407,19229237017,20353675917,23391840285,61425966,SRX13476317,SRS11373160,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00318,0.74297,0.003,0.07874,0.99969,0.83481,0.6,0.58428,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
64513,SRR17299056,SRX13476316,SRS11373159,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 24hpf COL50,GSM5746861,,source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 24hpf COL50,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 24hpf sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:24 hours|tissue:whole organism,GSM5746861,GSM5746861: Microwell seq datasets of Zebrafish 24hpf COL50; Danio rerio; RNA Seq,GSM5746861,,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,,assembly:GRCz11|intentional duplicate,Zebrafish_24hpf_COL50.bam,bam,93180912216.0,535522484.0,GSM5746861 r1,0:24 1:150,A:27511179288;C:19943495783;G:21163186103;T:24482014463;N:81036579,24,150,,,27511179288,19943495783,21163186103,24482014463,81036579,SRX13476316,SRS11373159,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00287,0.73081,0.00269,0.08165,0.99969,0.83469,0.53333,0.56313,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
76526,SRR25007131,SRX20762489,SRS18050783,SRP445520,PRJNA986875,Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish,GSE235668,Transcriptome Analysis,Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues  but their identification and organogenesis related function have not elucidated. In this study  high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos  which were important for zebrafish muscle development. The three stages were 10 hpf T1  24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10  24  36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.,,pubmed:38542412,,T3 1,GSM7507240,,source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:36hpf|geo loc name:missing|collection date:missing,T3 1,The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched  quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co.  Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Embryos,,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:Embryos|genotype:WT|developmental stage:36hpf,GSM7507240,GSM7507240: T3 1; Danio rerio; RNA Seq,GSM7507240 r1,GSM7507240,1,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP445520,,,T3_1.R1.fq.gz T3_1.R2.fq.gz,fastq fastq,15316392300.0,51054641.0,GSM7507240 r1,0:150 1:150,A:3880671888;C:3784758050;G:3856071137;T:3794810224;N:81001,150,150,,,3880671888,3784758050,3856071137,3794810224,81001,SRX20762489,SRS18050783,SRA1661372,henan normal university,henan normal university,2,0.41572,0.57842,0.09076,0.13329,0.79385,0.76142,0.43528,0.43567,150,150,B,B,mate1-mate2 similar by mapping diff,bgi,bgi,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,China,2023-06-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
76529,SRR25007134,SRX20762486,SRS18050778,SRP445520,PRJNA986875,Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish,GSE235668,Transcriptome Analysis,Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues  but their identification and organogenesis related function have not elucidated. In this study  high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos  which were important for zebrafish muscle development. The three stages were 10 hpf T1  24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10  24  36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.,,pubmed:38542412,,T2 1,GSM7507238,,source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:24hpf|geo loc name:missing|collection date:missing,T2 1,The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched  quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co.  Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Embryos,,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:Embryos|genotype:WT|developmental stage:24hpf,GSM7507238,GSM7507238: T2 1; Danio rerio; RNA Seq,GSM7507238 r1,GSM7507238,1,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP445520,,,T2_1.R2.fq.gz T2_1.R1.fq.gz,fastq fastq,14649880200.0,48832934.0,GSM7507238 r1,0:150 1:150,A:3695224943;C:3636149584;G:3688479871;T:3629948859;N:76943,150,150,,,3695224943,3636149584,3688479871,3629948859,76943,SRX20762486,SRS18050778,SRA1661372,henan normal university,henan normal university,2,0.43452,0.60496,0.08789,0.13132,0.7862,0.7528,0.44881,0.45341,150,150,B,B,mate1-mate2 similar by mapping diff,bgi,bgi,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,China,2023-06-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
76530,SRR25007135,SRX20762485,SRS18050780,SRP445520,PRJNA986875,Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish,GSE235668,Transcriptome Analysis,Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues  but their identification and organogenesis related function have not elucidated. In this study  high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos  which were important for zebrafish muscle development. The three stages were 10 hpf T1  24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10  24  36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.,,pubmed:38542412,,T2 2,GSM7507239,,source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:24hpf|geo loc name:missing|collection date:missing,T2 2,The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched  quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co.  Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Embryos,,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:Embryos|genotype:WT|developmental stage:24hpf,GSM7507239,GSM7507239: T2 2; Danio rerio; RNA Seq,GSM7507239 r1,GSM7507239,1,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP445520,,,T2_2.R1.fq.gz T2_2.R2.fq.gz,fastq fastq,14696199900.0,48987333.0,GSM7507239 r1,0:150 1:150,A:3735683721;C:3615176348;G:3714335362;T:3630926317;N:78152,150,150,,,3735683721,3615176348,3714335362,3630926317,78152,SRX20762485,SRS18050780,SRA1661372,henan normal university,henan normal university,2,0.42139,0.57658,0.08829,0.1292,0.78831,0.75617,0.44949,0.45776,150,150,B,B,mate1-mate2 similar by mapping diff,bgi,bgi,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,China,2023-06-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
76531,SRR25007136,SRX20762484,SRS18050779,SRP445520,PRJNA986875,Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish,GSE235668,Transcriptome Analysis,Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues  but their identification and organogenesis related function have not elucidated. In this study  high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos  which were important for zebrafish muscle development. The three stages were 10 hpf T1  24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10  24  36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.,,pubmed:38542412,,T3 2,GSM7507241,,source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:36hpf|geo loc name:missing|collection date:missing,T3 2,The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched  quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co.  Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Embryos,,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction.,,tissue:Embryos|genotype:WT|developmental stage:36hpf,GSM7507241,GSM7507241: T3 2; Danio rerio; RNA Seq,GSM7507241 r1,GSM7507241,1,Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen  cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit  Catalog NO. MRZG12324  Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP445520,,,T3_2.R2.fq.gz T3_2.R1.fq.gz,fastq fastq,15346908000.0,51156360.0,GSM7507241 r1,0:150 1:150,A:3937027213;C:3752697817;G:3796118846;T:3860983131;N:80993,150,150,,,3937027213,3752697817,3796118846,3860983131,80993,SRX20762484,SRS18050779,SRA1661372,henan normal university,henan normal university,2,0.4823,0.64213,0.10848,0.15245,0.77966,0.74752,0.43616,0.43697,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,China,2023-06-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures