{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"dropseq\" and tissue_curation_coarse = \"All anatomical structures\"", "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 . 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:GSM2838532", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP124289", null, "dangling references:treat as unmapped", "ZFOBLONG-DS5b.bam", "bam", 196960038.0, 3732948.0, "GSM2838532 r1", "0:52.76", "A:59884724;C:41040872;G:44343848;T:51548840;N:141754", 52, null, null, null, 59884724, 41040872, 44343848, 51548840, 141754, "SRX3367885", "SRS2665527", "SRA628740", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.9008, null, 0.0487, null, 0.83333, null, 0.69396, null, 26, 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"], [44504, "SRR6261602", "SRX3367884", "SRS2665526", "SRP124289", "PRJNA417290", "Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints", "GSE106474", "Transcriptome Analysis", "Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5.", "parent bioproject:PRJNA417291", "pubmed:29700225", 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"]], "truncated": false, 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