{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", experiment.platform = \"ILLUMINA\" and technology = \"dropseq\"", "rows": [[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", null, "WT zebrafish embryo shield Rep 1", "GSM2838533", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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 . 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Samples were combined and sequenced in batches DS2 DS5.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "WT zebrafish embryo oblong Rep 2", "GSM2838532", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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 . 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Samples were combined and sequenced in batches DS2 DS5.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "WT zebrafish embryo oblong Rep 1", "GSM2838531", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838531", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1334141601, 893306177, 989357821, 1127952860, 577703, "SRX3367884", "SRS2665526", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.88987, null, 0.04135, null, 0.88444, null, 0.69674, null, 30, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo high Rep 2", "GSM2838530", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838530", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 222013994, 149289044, 161706547, 203898449, 129967, "SRX3367883", "SRS2665524", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.82793, null, 0.04496, null, 0.82593, null, 0.64576, null, 37, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo high Rep 1", "GSM2838529", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 355328611, 231282565, 256994557, 306435407, 152131, "SRX3367882", "SRS2665523", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.88537, null, 0.04181, null, 0.87371, null, 0.67546, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo dome Rep 1", "GSM2838528", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 917833789, 596671084, 649280401, 821959372, 405728, "SRX3367881", "SRS2665525", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.87678, null, 0.05628, null, 0.88937, null, 0.37085, null, 44, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo bud Rep 4", "GSM2838527", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1923004447, 1355829109, 1430733445, 1734702312, 5969105, "SRX3367880", "SRS2665522", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.88781, null, 0.09347, null, 0.84358, null, 0.63177, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo bud Rep 3", "GSM2838526", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 3735824308, 2614320755, 2828705000, 3402591139, 8059482, "SRX3367879", "SRS2665521", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90065, null, 0.08373, null, 0.82716, null, 0.64737, null, 39, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo bud Rep 2", "GSM2838525", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1201317525, 820872807, 873362887, 1027226159, 88897, "SRX3367878", "SRS2665520", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.91489, null, 0.07264, null, 0.84684, null, 0.68127, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo bud Rep 1", "GSM2838524", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 591046898, 412519355, 441566116, 516943702, 867003, "SRX3367877", "SRS2665519", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.91352, null, 0.10693, null, 0.82921, null, 0.62781, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 90% epiboly Rep 3", "GSM2838523", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1463148609, 1002649035, 1087078720, 1284643937, 5321966, "SRX3367876", "SRS2665517", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90073, null, 0.07593, null, 0.85656, null, 0.66721, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 90% epiboly Rep 2", "GSM2838522", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838522", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1786246386, 1223369366, 1319845082, 1598104737, 4545872, "SRX3367875", "SRS2665518", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90983, null, 0.07417, null, 0.84887, null, 0.69062, null, 41, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 90% epiboly Rep 1", "GSM2838521", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 2915813449, 1944788007, 2074752689, 2470632938, 7113492, "SRX3367874", "SRS2665514", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90701, null, 0.09183, null, 0.84997, null, 0.70905, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 75% epiboly Rep 3", "GSM2838520", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838520", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1146132665, 796349091, 856725624, 1112518655, 3863989, "SRX3367873", "SRS2665516", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89527, null, 0.06395, null, 0.85395, null, 0.61881, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 75% epiboly Rep 2", "GSM2838519", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838519", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1860503244, 1298121538, 1397241096, 1699896990, 4912122, "SRX3367872", "SRS2665513", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90879, null, 0.05607, null, 0.849, null, 0.64494, null, 34, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 75% epiboly Rep 1", "GSM2838518", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838518", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 3844536415, 2601284821, 2774529684, 3284967732, 10312627, "SRX3367871", "SRS2665512", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.91618, null, 0.08367, null, 0.85695, null, 0.69056, null, 19, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 6 somite Rep 2", "GSM2838517", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838517", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1682994930, 1124480753, 1213976098, 1459811169, 1868366, "SRX3367870", "SRS2665511", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89126, null, 0.1186, null, 0.85476, null, 0.62994, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 6 somite Rep 1", "GSM2838516", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838516", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 2045470046, 1445282146, 1551331939, 1725694334, 2400663, "SRX3367869", "SRS2665510", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90931, null, 0.06771, null, 0.88306, null, 0.62745, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 60% epiboly Rep 3", "GSM2838515", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838515", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1148249585, 778428304, 832463962, 1070132046, 4611779, "SRX3367868", "SRS2665515", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89639, null, 0.05633, null, 0.87184, null, 0.71167, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 60% epiboly Rep 2", "GSM2838514", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838514", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1131311970, 778039231, 843841278, 1054333041, 3976862, "SRX3367867", "SRS2665509", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.8997, null, 0.05901, null, 0.85271, null, 0.66877, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 60% epiboly Rep 1", "GSM2838513", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838513", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 2840380863, 1954270941, 2115387210, 2512438103, 4890730, "SRX3367866", "SRS2665508", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90013, null, 0.10453, null, 0.84609, null, 0.67284, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 50% epiboly Rep 4", "GSM2838512", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838512", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1237706491, 863592991, 927386153, 1211073503, 4639076, "SRX3367865", "SRS2665505", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.87107, null, 0.04987, null, 0.85255, null, 0.64831, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 50% epiboly Rep 3", "GSM2838511", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838511", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1290955423, 877486318, 942860908, 1162275878, 4630512, "SRX3367864", "SRS2665503", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.88164, null, 0.04985, null, 0.85522, null, 0.68333, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 50% epiboly Rep 2", "GSM2838510", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838510", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1070153581, 717648649, 775104021, 935318712, 3659868, "SRX3367863", "SRS2665507", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89876, null, 0.05026, null, 0.85839, null, 0.7398, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 50% epiboly Rep 1", "GSM2838509", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838509", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 2652144410, 1801595414, 1947473372, 2284385129, 7180682, "SRX3367862", "SRS2665506", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.91106, null, 0.07336, null, 0.8356, null, 0.67412, null, 50, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo 3 somite Rep 1", "GSM2838508", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838508", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 1302285155, 910804445, 1019986862, 1087802148, 1392787, "SRX3367861", "SRS2665502", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.88196, null, 0.09807, null, 0.89585, null, 0.68342, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo zfs:0000015 Rep 2", "GSM2838507", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838507", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 430563775, 297250590, 322830484, 375658913, 1016310, "SRX3367860", "SRS2665504", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89678, null, 0.06492, null, 0.85403, null, 0.67064, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "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", null, "WT zebrafish embryo zfs:0000015 Rep 1", "GSM2838506", null, "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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C 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", null, "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\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "GEO Accession:GSM2838506", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "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, null, null, null, 477897847, 307865773, 330036592, 390748777, 257988, "SRX3367859", "SRS2665539", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.90526, null, 0.05376, null, 0.8644, null, 0.75191, null, 43, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "United States", "2017-11-02", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [56879, "SRR11164691", "SRX7789375", "SRS6204773", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Wt brain 8 dpf", "GSM4333122", null, "tissue:Wt brain 8 dpf dpf", "Zebrafish Wt brain 8 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Wt brain 8 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. EPI 00649 2019", "tissue:brain|genotype:WT|age:8 dpf", "GSM4333122", "GSM4333122: Zebrafish Wt brain 8 dpf Danio rerio; RNA Seq", "GSM4333122", null, "1", "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "8DPF4_S2_R1_001.fastq.gz 8DPF4_S2_R2_001.fastq.gz", "fastq fastq", 13384328000.0, 167304100.0, "GSM4333122 r1", "0:20 1:60", "A:3888292440;C:2947715560;G:3180865817;T:3366553945;N:900238", 20, 60, null, null, 3888292440, 2947715560, 3180865817, 3366553945, 900238, "SRX7789375", "SRS6204773", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01406, 0.88627, 0.00662, 0.16845, 0.98768, 0.79058, 0.70669, 0.62062, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [56880, "SRR11164690", "SRX7789374", "SRS6204772", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Mutscn1Lab brain 8 dpf", "GSM4333121", null, "tissue:Mutscn1Lab brain 8 dpf dpf", "Zebrafish Mutscn1Lab brain 8 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Mutscn1Lab brain 8 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. 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Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "8DPF3_S1_R1_001.fastq.gz 8DPF3_S1_R2_001.fastq.gz", "fastq fastq", 9580350080.0, 119754376.0, "GSM4333121 r1", "0:20 1:60", "A:2809490643;C:2102026943;G:2303250077;T:2364936390;N:646027", 20, 60, null, null, 2809490643, 2102026943, 2303250077, 2364936390, 646027, "SRX7789374", "SRS6204772", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01149, 0.9048, 0.00587, 0.15201, 0.98979, 0.79283, 0.6829, 0.63091, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [56881, "SRR11164689", "SRX7789373", "SRS6204771", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Mutscn1Lab brain 5 dpf", "GSM4333120", null, "tissue:Mutscn1Lab brain 5 dpf dpf", "Zebrafish Mutscn1Lab brain 5 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Mutscn1Lab brain 5 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. 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Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "5DPF2_S2_R1_001.fastq.gz 5DPF2_S2_R2_001.fastq.gz", "fastq fastq", 6663274080.0, 83290926.0, "GSM4333120 r1", "0:20 1:60", "A:1851799411;C:1470225216;G:1666931688;T:1673879241;N:438524", 20, 60, null, null, 1851799411, 1470225216, 1666931688, 1673879241, 438524, "SRX7789373", "SRS6204771", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01151, 0.90584, 0.00724, 0.13592, 0.99022, 0.84784, 0.40101, 0.60276, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [56882, "SRR11164688", "SRX7789372", "SRS6204770", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Wt brain 5 dpf", "GSM4333119", null, "tissue:Wt brain 5 dpf dpf", "Zebrafish Wt brain 5 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Wt brain 5 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. 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