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
44518,SRR6261588,SRX3367870,SRS2665511,SRP124289,PRJNA417290,Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints,GSE106474,Transcriptome Analysis,Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged  mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5.,parent bioproject:PRJNA417291,pubmed:29700225,,WT zebrafish embryo 6 somite  Rep 2,GSM2838517,,tissue:Wild type TLAB Embryo|developmental stage:6 somite|hpf batch:DS5,WT zebrafish embryo 6 somite  Rep 2,Data was processed using Drop seq tools v1.01  according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells  and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts,Wild type TLAB Embryo,,Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015  with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.,Tupful longfin / AB TLAB fish were incrossed  embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging.,developmental stage:6 somite|hpf batch:DS5,GSM2838517,GSM2838517: WT zebrafish embryo 6 somite  Rep 2; Danio rerio; RNA Seq,GSM2838517,,1,Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015  with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.,GEO Accession:GSM2838517,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF6S-DS5b.bam,bam,5483131316.0,97533075.0,GSM2838517 r1,0:56.22,A:1682994930;C:1124480753;G:1213976098;T:1459811169;N:1868366,56,,,,1682994930,1124480753,1213976098,1459811169,1868366,SRX3367870,SRS2665511,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.89126,,0.1186,,0.85476,,0.62994,,62,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
44519,SRR6261587,SRX3367869,SRS2665510,SRP124289,PRJNA417290,Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints,GSE106474,Transcriptome Analysis,Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged  mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5.,parent bioproject:PRJNA417291,pubmed:29700225,,WT zebrafish embryo 6 somite  Rep 1,GSM2838516,,tissue:Wild type TLAB Embryo|developmental stage:6 somite|hpf batch:DS5,WT zebrafish embryo 6 somite  Rep 1,Data was processed using Drop seq tools v1.01  according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells  and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts,Wild type TLAB Embryo,,Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015  with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.,Tupful longfin / AB TLAB fish were incrossed  embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging.,developmental stage:6 somite|hpf batch:DS5,GSM2838516,GSM2838516: WT zebrafish embryo 6 somite  Rep 1; Danio rerio; RNA Seq,GSM2838516,,1,Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015  with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.,GEO Accession:GSM2838516,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF6S-DS5.bam,bam,6770179128.0,120219927.0,GSM2838516 r1,0:56.31,A:2045470046;C:1445282146;G:1551331939;T:1725694334;N:2400663,56,,,,2045470046,1445282146,1551331939,1725694334,2400663,SRX3367869,SRS2665510,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90931,,0.06771,,0.88306,,0.62745,,62,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
44527,SRR6261579,SRX3367861,SRS2665502,SRP124289,PRJNA417290,Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints,GSE106474,Transcriptome Analysis,Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged  mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5.,parent bioproject:PRJNA417291,pubmed:29700225,,WT zebrafish embryo 3 somite  Rep 1,GSM2838508,,tissue:Wild type TLAB Embryo|developmental stage:3 somite|hpf batch:DS5,WT zebrafish embryo 3 somite  Rep 1,Data was processed using Drop seq tools v1.01  according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells  and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts,Wild type TLAB Embryo,,Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015  with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.,Tupful longfin / AB TLAB fish were incrossed  embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging.,developmental stage:3 somite|hpf batch:DS5,GSM2838508,GSM2838508: WT zebrafish embryo 3 somite  Rep 1; Danio rerio; RNA Seq,GSM2838508,,1,Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015  with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.,GEO Accession:GSM2838508,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF3S-DS5.bam,bam,4322271397.0,76613226.0,GSM2838508 r1,0:56.42,A:1302285155;C:910804445;G:1019986862;T:1087802148;N:1392787,56,,,,1302285155,910804445,1019986862,1087802148,1392787,SRX3367861,SRS2665502,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.88196,,0.09807,,0.89585,,0.68342,,62,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Segmentation,Embryo,Embryo Imprecise,All anatomical structures