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
44505,SRR6261601,SRX3367883,SRS2665524,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 high  Rep 2,GSM2838530,,tissue:Wild type TLAB Embryo|developmental stage:high|hpf batch:DS5,WT zebrafish embryo high  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:high|hpf batch:DS5,GSM2838530,GSM2838530: WT zebrafish embryo high  Rep 2; Danio rerio; RNA Seq,GSM2838530,,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:GSM2838530,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFHIGH-DS5b.bam,bam,737038001.0,12994158.0,GSM2838530 r1,0:56.72,A:222013994;C:149289044;G:161706547;T:203898449;N:129967,56,,,,222013994,149289044,161706547,203898449,129967,SRX3367883,SRS2665524,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.82793,,0.04496,,0.82593,,0.64576,,37,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
44506,SRR6261600,SRX3367882,SRS2665523,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 high  Rep 1,GSM2838529,,tissue:Wild type TLAB Embryo|developmental stage:high|hpf batch:DS5,WT zebrafish embryo high  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:high|hpf batch:DS5,GSM2838529,GSM2838529: WT zebrafish embryo high  Rep 1; Danio rerio; RNA Seq,GSM2838529,,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:GSM2838529,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFHIGH-DS5.bam,bam,1150193271.0,19592509.0,GSM2838529 r1,0:58.71,A:355328611;C:231282565;G:256994557;T:306435407;N:152131,58,,,,355328611,231282565,256994557,306435407,152131,SRX3367882,SRS2665523,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.88537,,0.04181,,0.87371,,0.67546,,62,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
44508,SRR6261598,SRX3367880,SRS2665522,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 bud  Rep 4,GSM2838527,,tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS4,WT zebrafish embryo bud  Rep 4,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:bud|hpf batch:DS4,GSM2838527,GSM2838527: WT zebrafish embryo bud  Rep 4; Danio rerio; RNA Seq,GSM2838527,,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:GSM2838527,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFB-DS4.bam,bam,6450238418.0,135245227.0,GSM2838527 r1,0:47.69,A:1923004447;C:1355829109;G:1430733445;T:1734702312;N:5969105,47,,,,1923004447,1355829109,1430733445,1734702312,5969105,SRX3367880,SRS2665522,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.88781,,0.09347,,0.84358,,0.63177,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
44509,SRR6261597,SRX3367879,SRS2665521,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 bud  Rep 3,GSM2838526,,tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS3,WT zebrafish embryo bud  Rep 3,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:bud|hpf batch:DS3,GSM2838526,GSM2838526: WT zebrafish embryo bud  Rep 3; Danio rerio; RNA Seq,GSM2838526,,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:GSM2838526,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFB-DS3.bam,bam,12589500684.0,264160754.0,GSM2838526 r1,0:47.66,A:3735824308;C:2614320755;G:2828705000;T:3402591139;N:8059482,47,,,,3735824308,2614320755,2828705000,3402591139,8059482,SRX3367879,SRS2665521,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90065,,0.08373,,0.82716,,0.64737,,39,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
44510,SRR6261596,SRX3367878,SRS2665520,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 bud  Rep 2,GSM2838525,,tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS2,WT zebrafish embryo bud  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:bud|hpf batch:DS2,GSM2838525,GSM2838525: WT zebrafish embryo bud  Rep 2; Danio rerio; RNA Seq,GSM2838525,,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:GSM2838525,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFB-DS2b.bam,bam,3922868275.0,82034280.0,GSM2838525 r1,0:47.82,A:1201317525;C:820872807;G:873362887;T:1027226159;N:88897,47,,,,1201317525,820872807,873362887,1027226159,88897,SRX3367878,SRS2665520,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.91489,,0.07264,,0.84684,,0.68127,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
44511,SRR6261595,SRX3367877,SRS2665519,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 bud  Rep 1,GSM2838524,,tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS2,WT zebrafish embryo bud  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:bud|hpf batch:DS2,GSM2838524,GSM2838524: WT zebrafish embryo bud  Rep 1; Danio rerio; RNA Seq,GSM2838524,,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:GSM2838524,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFB-DS2.bam,bam,1962943074.0,40871825.0,GSM2838524 r1,0:48.03,A:591046898;C:412519355;G:441566116;T:516943702;N:867003,48,,,,591046898,412519355,441566116,516943702,867003,SRX3367877,SRS2665519,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.91352,,0.10693,,0.82921,,0.62781,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Undetermined,Embryo,Embryo Imprecise,All anatomical structures