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
44502,SRR6261604,SRX3367886,SRS2665528,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 shield  Rep 1,GSM2838533,,tissue:Wild type TLAB Embryo|developmental stage:shield|hpf batch:DS5,WT zebrafish embryo shield  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:shield|hpf batch:DS5,GSM2838533,GSM2838533: WT zebrafish embryo shield  Rep 1; Danio rerio; RNA Seq,GSM2838533,,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:GSM2838533,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFS-DS5.bam,bam,3179843792.0,55979578.0,GSM2838533 r1,0:56.80,A:961841501;C:638551921;G:690013778;T:888532131;N:904461,56,,,,961841501,638551921,690013778,888532131,904461,SRX3367886,SRS2665528,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90259,,0.05737,,0.88183,,0.63826,,39,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44503,SRR6261603,SRX3367885,SRS2665527,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 oblong  Rep 2,GSM2838532,,tissue:Wild type TLAB Embryo|developmental stage:oblong|hpf batch:DS5,WT zebrafish embryo oblong  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:oblong|hpf batch:DS5,GSM2838532,GSM2838532: WT zebrafish embryo oblong  Rep 2; Danio rerio; RNA Seq,GSM2838532,,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:GSM2838532,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFOBLONG-DS5b.bam,bam,196960038.0,3732948.0,GSM2838532 r1,0:52.76,A:59884724;C:41040872;G:44343848;T:51548840;N:141754,52,,,,59884724,41040872,44343848,51548840,141754,SRX3367885,SRS2665527,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.9008,,0.0487,,0.83333,,0.69396,,26,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44504,SRR6261602,SRX3367884,SRS2665526,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 oblong  Rep 1,GSM2838531,,tissue:Wild type TLAB Embryo|developmental stage:oblong|hpf batch:DS5,WT zebrafish embryo oblong  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:oblong|hpf batch:DS5,GSM2838531,GSM2838531: WT zebrafish embryo oblong  Rep 1; Danio rerio; RNA Seq,GSM2838531,,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:GSM2838531,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFOBLONG-DS5.bam,bam,4345336162.0,73291146.0,GSM2838531 r1,0:59.29,A:1334141601;C:893306177;G:989357821;T:1127952860;N:577703,59,,,,1334141601,893306177,989357821,1127952860,577703,SRX3367884,SRS2665526,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.88987,,0.04135,,0.88444,,0.69674,,30,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Blastula,Embryo,Embryo Imprecise,All anatomical structures
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
44507,SRR6261599,SRX3367881,SRS2665525,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 dome  Rep 1,GSM2838528,,tissue:Wild type TLAB Embryo|developmental stage:dome|hpf batch:DS5,WT zebrafish embryo dome  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:dome|hpf batch:DS5,GSM2838528,GSM2838528: WT zebrafish embryo dome  Rep 1; Danio rerio; RNA Seq,GSM2838528,,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:GSM2838528,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZFDOME-DS5.bam,bam,2986150374.0,51431163.0,GSM2838528 r1,0:58.06,A:917833789;C:596671084;G:649280401;T:821959372;N:405728,58,,,,917833789,596671084,649280401,821959372,405728,SRX3367881,SRS2665525,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.87678,,0.05628,,0.88937,,0.37085,,44,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Blastula,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
44512,SRR6261594,SRX3367876,SRS2665517,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 90% epiboly  Rep 3,GSM2838523,,tissue:Wild type TLAB Embryo|developmental stage:90% epiboly|hpf batch:DS4,WT zebrafish embryo 90% epiboly  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:90% epiboly|hpf batch:DS4,GSM2838523,GSM2838523: WT zebrafish embryo 90% epiboly  Rep 3; Danio rerio; RNA Seq,GSM2838523,,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:GSM2838523,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF90-DS4.bam,bam,4842842267.0,101293760.0,GSM2838523 r1,0:47.81,A:1463148609;C:1002649035;G:1087078720;T:1284643937;N:5321966,47,,,,1463148609,1002649035,1087078720,1284643937,5321966,SRX3367876,SRS2665517,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90073,,0.07593,,0.85656,,0.66721,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44513,SRR6261593,SRX3367875,SRS2665518,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 90% epiboly  Rep 2,GSM2838522,,tissue:Wild type TLAB Embryo|developmental stage:90% epiboly|hpf batch:DS3,WT zebrafish embryo 90% epiboly  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:90% epiboly|hpf batch:DS3,GSM2838522,GSM2838522: WT zebrafish embryo 90% epiboly  Rep 2; Danio rerio; RNA Seq,GSM2838522,,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:GSM2838522,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF90-DS3.bam,bam,5932111443.0,123808277.0,GSM2838522 r1,0:47.91,A:1786246386;C:1223369366;G:1319845082;T:1598104737;N:4545872,47,,,,1786246386,1223369366,1319845082,1598104737,4545872,SRX3367875,SRS2665518,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90983,,0.07417,,0.84887,,0.69062,,41,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44514,SRR6261592,SRX3367874,SRS2665514,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 90% epiboly  Rep 1,GSM2838521,,tissue:Wild type TLAB Embryo|developmental stage:90% epiboly|hpf batch:DS2,WT zebrafish embryo 90% epiboly  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:90% epiboly|hpf batch:DS2,GSM2838521,GSM2838521: WT zebrafish embryo 90% epiboly  Rep 1; Danio rerio; RNA Seq,GSM2838521,,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:GSM2838521,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF90-DS2.bam,bam,9413100575.0,196594599.0,GSM2838521 r1,0:47.88,A:2915813449;C:1944788007;G:2074752689;T:2470632938;N:7113492,47,,,,2915813449,1944788007,2074752689,2470632938,7113492,SRX3367874,SRS2665514,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90701,,0.09183,,0.84997,,0.70905,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44515,SRR6261591,SRX3367873,SRS2665516,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 75% epiboly  Rep 3,GSM2838520,,tissue:Wild type TLAB Embryo|developmental stage:75% epiboly|hpf batch:DS4,WT zebrafish embryo 75% epiboly  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:75% epiboly|hpf batch:DS4,GSM2838520,GSM2838520: WT zebrafish embryo 75% epiboly  Rep 3; Danio rerio; RNA Seq,GSM2838520,,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:GSM2838520,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF75-DS4.bam,bam,3915590024.0,82098818.0,GSM2838520 r1,0:47.69,A:1146132665;C:796349091;G:856725624;T:1112518655;N:3863989,47,,,,1146132665,796349091,856725624,1112518655,3863989,SRX3367873,SRS2665516,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.89527,,0.06395,,0.85395,,0.61881,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44516,SRR6261590,SRX3367872,SRS2665513,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 75% epiboly  Rep 2,GSM2838519,,tissue:Wild type TLAB Embryo|developmental stage:75% epiboly|hpf batch:DS3,WT zebrafish embryo 75% epiboly  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:75% epiboly|hpf batch:DS3,GSM2838519,GSM2838519: WT zebrafish embryo 75% epiboly  Rep 2; Danio rerio; RNA Seq,GSM2838519,,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:GSM2838519,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF75-DS3.bam,bam,6260674990.0,130686591.0,GSM2838519 r1,0:47.91,A:1860503244;C:1298121538;G:1397241096;T:1699896990;N:4912122,47,,,,1860503244,1298121538,1397241096,1699896990,4912122,SRX3367872,SRS2665513,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90879,,0.05607,,0.849,,0.64494,,34,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44517,SRR6261589,SRX3367871,SRS2665512,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 75% epiboly  Rep 1,GSM2838518,,tissue:Wild type TLAB Embryo|developmental stage:75% epiboly|hpf batch:DS2,WT zebrafish embryo 75% epiboly  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:75% epiboly|hpf batch:DS2,GSM2838518,GSM2838518: WT zebrafish embryo 75% epiboly  Rep 1; Danio rerio; RNA Seq,GSM2838518,,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:GSM2838518,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF75-DS2.bam,bam,12515631279.0,259899014.0,GSM2838518 r1,0:48.16,A:3844536415;C:2601284821;G:2774529684;T:3284967732;N:10312627,48,,,,3844536415,2601284821,2774529684,3284967732,10312627,SRX3367871,SRS2665512,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.91618,,0.08367,,0.85695,,0.69056,,19,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
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
44520,SRR6261586,SRX3367868,SRS2665515,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 60% epiboly  Rep 3,GSM2838515,,tissue:Wild type TLAB Embryo|developmental stage:60% epiboly|hpf batch:DS4,WT zebrafish embryo 60% epiboly  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:60% epiboly|hpf batch:DS4,GSM2838515,GSM2838515: WT zebrafish embryo 60% epiboly  Rep 3; Danio rerio; RNA Seq,GSM2838515,,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:GSM2838515,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF60-DS4.bam,bam,3833885676.0,80339895.0,GSM2838515 r1,0:47.72,A:1148249585;C:778428304;G:832463962;T:1070132046;N:4611779,47,,,,1148249585,778428304,832463962,1070132046,4611779,SRX3367868,SRS2665515,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.89639,,0.05633,,0.87184,,0.71167,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44521,SRR6261585,SRX3367867,SRS2665509,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 60% epiboly  Rep 2,GSM2838514,,tissue:Wild type TLAB Embryo|developmental stage:60% epiboly|hpf batch:DS3,WT zebrafish embryo 60% epiboly  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:60% epiboly|hpf batch:DS3,GSM2838514,GSM2838514: WT zebrafish embryo 60% epiboly  Rep 2; Danio rerio; RNA Seq,GSM2838514,,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:GSM2838514,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF60-DS3.bam,bam,3811502382.0,80015031.0,GSM2838514 r1,0:47.63,A:1131311970;C:778039231;G:843841278;T:1054333041;N:3976862,47,,,,1131311970,778039231,843841278,1054333041,3976862,SRX3367867,SRS2665509,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.8997,,0.05901,,0.85271,,0.66877,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44522,SRR6261584,SRX3367866,SRS2665508,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 60% epiboly  Rep 1,GSM2838513,,tissue:Wild type TLAB Embryo|developmental stage:60% epiboly|hpf batch:DS2,WT zebrafish embryo 60% epiboly  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:60% epiboly|hpf batch:DS2,GSM2838513,GSM2838513: WT zebrafish embryo 60% epiboly  Rep 1; Danio rerio; RNA Seq,GSM2838513,,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:GSM2838513,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF60-DS2.bam,bam,9427367847.0,197041685.0,GSM2838513 r1,0:47.84,A:2840380863;C:1954270941;G:2115387210;T:2512438103;N:4890730,47,,,,2840380863,1954270941,2115387210,2512438103,4890730,SRX3367866,SRS2665508,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90013,,0.10453,,0.84609,,0.67284,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44523,SRR6261583,SRX3367865,SRS2665505,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 50% epiboly  Rep 4,GSM2838512,,tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS4,WT zebrafish embryo 50% epiboly  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:50% epiboly|hpf batch:DS4,GSM2838512,GSM2838512: WT zebrafish embryo 50% epiboly  Rep 4; Danio rerio; RNA Seq,GSM2838512,,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:GSM2838512,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF50-DS4b.bam,bam,4244398214.0,89440689.0,GSM2838512 r1,0:47.45,A:1237706491;C:863592991;G:927386153;T:1211073503;N:4639076,47,,,,1237706491,863592991,927386153,1211073503,4639076,SRX3367865,SRS2665505,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.87107,,0.04987,,0.85255,,0.64831,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44524,SRR6261582,SRX3367864,SRS2665503,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 50% epiboly  Rep 3,GSM2838511,,tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS4,WT zebrafish embryo 50% epiboly  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:50% epiboly|hpf batch:DS4,GSM2838511,GSM2838511: WT zebrafish embryo 50% epiboly  Rep 3; Danio rerio; RNA Seq,GSM2838511,,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:GSM2838511,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF50-DS4.bam,bam,4278209039.0,89476992.0,GSM2838511 r1,0:47.81,A:1290955423;C:877486318;G:942860908;T:1162275878;N:4630512,47,,,,1290955423,877486318,942860908,1162275878,4630512,SRX3367864,SRS2665503,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.88164,,0.04985,,0.85522,,0.68333,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44525,SRR6261581,SRX3367863,SRS2665507,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 50% epiboly  Rep 2,GSM2838510,,tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS3,WT zebrafish embryo 50% epiboly  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:50% epiboly|hpf batch:DS3,GSM2838510,GSM2838510: WT zebrafish embryo 50% epiboly  Rep 2; Danio rerio; RNA Seq,GSM2838510,,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:GSM2838510,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF50-DS3.bam,bam,3501884831.0,73345396.0,GSM2838510 r1,0:47.75,A:1070153581;C:717648649;G:775104021;T:935318712;N:3659868,47,,,,1070153581,717648649,775104021,935318712,3659868,SRX3367863,SRS2665507,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.89876,,0.05026,,0.85839,,0.7398,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
44526,SRR6261580,SRX3367862,SRS2665506,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 50% epiboly  Rep 1,GSM2838509,,tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS2,WT zebrafish embryo 50% epiboly  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:50% epiboly|hpf batch:DS2,GSM2838509,GSM2838509: WT zebrafish embryo 50% epiboly  Rep 1; Danio rerio; RNA Seq,GSM2838509,,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:GSM2838509,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF50-DS2.bam,bam,8692779007.0,181078327.0,GSM2838509 r1,0:48.01,A:2652144410;C:1801595414;G:1947473372;T:2284385129;N:7180682,48,,,,2652144410,1801595414,1947473372,2284385129,7180682,SRX3367862,SRS2665506,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.91106,,0.07336,,0.8356,,0.67412,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Gastrula,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
44528,SRR6261578,SRX3367860,SRS2665504,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 zfs:0000015  Rep 2,GSM2838507,,tissue:Wild type TLAB Embryo|developmental stage:zfs:0000015|hpf batch:DS5,WT zebrafish embryo zfs:0000015  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:zfs:0000015|hpf batch:DS5,GSM2838507,GSM2838507: WT zebrafish embryo zfs:0000015  Rep 2; Danio rerio; RNA Seq,GSM2838507,,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:GSM2838507,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF30-DS5b.bam,bam,1427320072.0,27100581.0,GSM2838507 r1,0:52.67,A:430563775;C:297250590;G:322830484;T:375658913;N:1016310,52,,,,430563775,297250590,322830484,375658913,1016310,SRX3367860,SRS2665504,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.89678,,0.06492,,0.85403,,0.67064,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Blastula,Embryo,Embryo Imprecise,All anatomical structures
44529,SRR6261577,SRX3367859,SRS2665539,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 zfs:0000015  Rep 1,GSM2838506,,tissue:Wild type TLAB Embryo|developmental stage:zfs:0000015|hpf batch:DS5,WT zebrafish embryo zfs:0000015  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:zfs:0000015|hpf batch:DS5,GSM2838506,GSM2838506: WT zebrafish embryo zfs:0000015  Rep 1; Danio rerio; RNA Seq,GSM2838506,,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:GSM2838506,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP124289,,dangling references:treat as unmapped,ZF30-DS5.bam,bam,1506806977.0,25842795.0,GSM2838506 r1,0:58.31,A:477897847;C:307865773;G:330036592;T:390748777;N:257988,58,,,,477897847,307865773,330036592,390748777,257988,SRX3367859,SRS2665539,SRA628740,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.90526,,0.05376,,0.8644,,0.75191,,43,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,dropseq,,United States,2017-11-02,Blastula,Embryo,Embryo Imprecise,All anatomical structures