{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"dropseq\"", "rows": [[44502, "SRR6261604", "SRX3367886", "SRS2665528", "SRP124289", "PRJNA417290", "Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints", "GSE106474", "Transcriptome Analysis", "Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "WT zebrafish embryo shield Rep 1", "GSM2838533", null, "tissue:Wild type TLAB Embryo|developmental stage:shield|hpf batch:DS5", "WT zebrafish embryo shield Rep 1", "Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts", "Wild type TLAB Embryo", null, "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C in chorions until they reached the desired stage confirmed via visual morphological staging.", "developmental stage:shield|hpf batch:DS5", "GSM2838533", "GSM2838533: WT zebrafish embryo shield Rep 1; Danio rerio; RNA Seq", "GSM2838533", null, "1", "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . 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Samples were combined and sequenced in batches DS2 DS5.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "WT zebrafish embryo oblong Rep 2", "GSM2838532", null, "tissue:Wild type TLAB Embryo|developmental stage:oblong|hpf batch:DS5", "WT zebrafish embryo oblong Rep 2", "Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts", "Wild type TLAB Embryo", null, "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12\u201313 cycles of PCR amplification and 50\u2013100 STAMPs per PCR reaction.", "Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28\u00b0C in chorions until they reached the desired stage confirmed via visual morphological staging.", "developmental stage:oblong|hpf batch:DS5", "GSM2838532", "GSM2838532: WT zebrafish embryo oblong Rep 2; Danio rerio; RNA Seq", "GSM2838532", null, "1", "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . 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"], [56879, "SRR11164691", "SRX7789375", "SRS6204773", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Wt brain 8 dpf", "GSM4333122", null, "tissue:Wt brain 8 dpf dpf", "Zebrafish Wt brain 8 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Wt brain 8 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. EPI 00649 2019", "tissue:brain|genotype:WT|age:8 dpf", "GSM4333122", "GSM4333122: Zebrafish Wt brain 8 dpf Danio rerio; RNA Seq", "GSM4333122", null, "1", "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "8DPF4_S2_R1_001.fastq.gz 8DPF4_S2_R2_001.fastq.gz", "fastq fastq", 13384328000.0, 167304100.0, "GSM4333122 r1", "0:20 1:60", "A:3888292440;C:2947715560;G:3180865817;T:3366553945;N:900238", 20, 60, null, null, 3888292440, 2947715560, 3180865817, 3366553945, 900238, "SRX7789375", "SRS6204773", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01406, 0.88627, 0.00662, 0.16845, 0.98768, 0.79058, 0.70669, 0.62062, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [56880, "SRR11164690", "SRX7789374", "SRS6204772", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Mutscn1Lab brain 8 dpf", "GSM4333121", null, "tissue:Mutscn1Lab brain 8 dpf dpf", "Zebrafish Mutscn1Lab brain 8 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Mutscn1Lab brain 8 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. EPI 00649 2019", "tissue:brain|genotype:scn1Lab|age:8 dpf", "GSM4333121", "GSM4333121: Zebrafish Mutscn1Lab brain 8 dpf Danio rerio; RNA Seq", "GSM4333121", null, "1", "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "8DPF3_S1_R1_001.fastq.gz 8DPF3_S1_R2_001.fastq.gz", "fastq fastq", 9580350080.0, 119754376.0, "GSM4333121 r1", "0:20 1:60", "A:2809490643;C:2102026943;G:2303250077;T:2364936390;N:646027", 20, 60, null, null, 2809490643, 2102026943, 2303250077, 2364936390, 646027, "SRX7789374", "SRS6204772", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01149, 0.9048, 0.00587, 0.15201, 0.98979, 0.79283, 0.6829, 0.63091, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [56881, "SRR11164689", "SRX7789373", "SRS6204771", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Mutscn1Lab brain 5 dpf", "GSM4333120", null, "tissue:Mutscn1Lab brain 5 dpf dpf", "Zebrafish Mutscn1Lab brain 5 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Mutscn1Lab brain 5 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. EPI 00649 2019", "tissue:brain|genotype:scn1Lab|age:5 dpf", "GSM4333120", "GSM4333120: Zebrafish Mutscn1Lab brain 5 dpf Danio rerio; RNA Seq", "GSM4333120", null, "1", "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "5DPF2_S2_R1_001.fastq.gz 5DPF2_S2_R2_001.fastq.gz", "fastq fastq", 6663274080.0, 83290926.0, "GSM4333120 r1", "0:20 1:60", "A:1851799411;C:1470225216;G:1666931688;T:1673879241;N:438524", 20, 60, null, null, 1851799411, 1470225216, 1666931688, 1673879241, 438524, "SRX7789373", "SRS6204771", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01151, 0.90584, 0.00724, 0.13592, 0.99022, 0.84784, 0.40101, 0.60276, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [56882, "SRR11164688", "SRX7789372", "SRS6204770", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Wt brain 5 dpf", "GSM4333119", null, "tissue:Wt brain 5 dpf dpf", "Zebrafish Wt brain 5 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Wt brain 5 dpf", null, "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al. EPI 00649 2019", "tissue:brain|genotype:WT|age:5 dpf", "GSM4333119", "GSM4333119: Zebrafish Wt brain 5 dpf Danio rerio; RNA Seq", "GSM4333119", null, "1", "Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333119", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "5DPF1_S1_R2_001.fastq.gz 5DPF1_S1_R1_001.fastq.gz", "fastq fastq", 6473128320.0, 80914104.0, "GSM4333119 r1", "0:20 1:60", "A:1828609493;C:1442384903;G:1561588918;T:1640121023;N:423983", 20, 60, null, null, 1828609493, 1442384903, 1561588918, 1640121023, 423983, "SRX7789372", "SRS6204770", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01235, 0.90642, 0.00683, 0.13484, 0.9892, 0.83956, 0.71539, 0.60611, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"], [72137, "SRR22266708", "SRX18243019", "SRS15738744", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "7 dpa replicate 31 scRNAseq", "GSM6727464", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "7 dpa replicate 31 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "GSM6727464", "GSM6727464: 7 dpa replicate 31 scRNAseq; Danio rerio; RNA Seq", "GSM6727464 r1", "GSM6727464", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11R_IO7720_S6_R1_001.fastq.gz 20200107_LIB11R_IO7720_S6_R2_001.fastq.gz", "fastq fastq", 4802290236.0, 64895814.0, "GSM6727464 r1", "0:25 1:49", "A:1351689314;C:1044099826;G:1084104790;T:1321739644;N:656662", 25, 49, null, null, 1351689314, 1044099826, 1084104790, 1321739644, 656662, "SRX18243019", "SRS15738744", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01055, 0.84852, 0.00192, 0.03717, 0.99527, 0.89234, 0.86731, 0.69661, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72138, "SRR22266709", "SRX18243018", "SRS15738743", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "3 dpa replicate 3 scRNAseq", "GSM6727463", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "3 dpa replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "GSM6727463", "GSM6727463: 3 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727463 r1", "GSM6727463", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11Q_IO7720_S5_R1_001.fastq.gz 20200107_LIB11Q_IO7720_S5_R2_001.fastq.gz", "fastq fastq", 4327529324.0, 58480126.0, "GSM6727463 r1", "0:25 1:49", "A:1223359778;C:914892543;G:970000561;T:1218683252;N:593190", 25, 49, null, null, 1223359778, 914892543, 970000561, 1218683252, 593190, "SRX18243018", "SRS15738743", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00899, 0.83745, 0.00188, 0.04633, 0.99431, 0.84492, 0.84148, 0.68261, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72139, "SRR22266710", "SRX18243017", "SRS15738742", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "2 dpa replicate 3 scRNAseq", "GSM6727462", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "2 dpa replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "GSM6727462", "GSM6727462: 2 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727462 r1", "GSM6727462", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11P_IO7720_S4_R1_001.fastq.gz 20200107_LIB11P_IO7720_S4_R2_001.fastq.gz", "fastq fastq", 5036062970.0, 68054905.0, "GSM6727462 r1", "0:25 1:49", "A:1410235407;C:1062242143;G:1134885588;T:1428020401;N:679431", 25, 49, null, null, 1410235407, 1062242143, 1134885588, 1428020401, 679431, "SRX18243017", "SRS15738742", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00859, 0.86477, 0.00193, 0.06588, 0.99387, 0.81124, 0.81235, 0.61962, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72140, "SRR22266711", "SRX18243016", "SRS15738741", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "1 dpa replicate 3 scRNAseq", "GSM6727461", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "1 dpa replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "GSM6727461", "GSM6727461: 1 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727461 r1", "GSM6727461", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11O_IO7720_S3_R1_001.fastq.gz 20200107_LIB11O_IO7720_S3_R2_001.fastq.gz", "fastq fastq", 4734982870.0, 63986255.0, "GSM6727461 r1", "0:25 1:49", "A:1350059086;C:986396540;G:1055462585;T:1342412482;N:652177", 25, 49, null, null, 1350059086, 986396540, 1055462585, 1342412482, 652177, "SRX18243016", "SRS15738741", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01072, 0.82414, 0.0025, 0.06977, 0.99159, 0.83004, 0.66346, 0.59359, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72141, "SRR22266712", "SRX18243015", "SRS15738740", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "0 dpa replicate 3 scRNAseq", "GSM6727460", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "0 dpa replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "GSM6727460", "GSM6727460: 0 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727460 r1", "GSM6727460", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11N_IO7720_S2_R1_001.fastq.gz 20200107_LIB11N_IO7720_S2_R2_001.fastq.gz", "fastq fastq", 4224737108.0, 57091042.0, "GSM6727460 r1", "0:25 1:49", "A:1171021854;C:919004861;G:955423740;T:1178700581;N:586072", 25, 49, null, null, 1171021854, 919004861, 955423740, 1178700581, 586072, "SRX18243015", "SRS15738740", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00691, 0.71165, 0.00186, 0.09225, 0.99634, 0.86354, 0.77015, 0.67507, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72142, "SRR22266713", "SRX18243014", "SRS15738739", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "mock replicate 3 scRNAseq", "GSM6727459", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "mock replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "GSM6727459", "GSM6727459: mock replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727459 r1", "GSM6727459", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11M_IO7720_S1_R1_001.fastq.gz 20200107_LIB11M_IO7720_S1_R2_001.fastq.gz", "fastq fastq", 4136407822.0, 55897403.0, "GSM6727459 r1", "0:25 1:49", "A:1196087924;C:868741250;G:928417059;T:1142590047;N:571542", 25, 49, null, null, 1196087924, 868741250, 928417059, 1142590047, 571542, "SRX18243014", "SRS15738739", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00992, 0.78, 0.00257, 0.11335, 0.99431, 0.83747, 0.75089, 0.69588, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72143, "SRR22266714", "SRX18243013", "SRS15738738", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "7 dpa replicate 2 scRNAseq", "GSM6727458", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "7 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "GSM6727458", "GSM6727458: 7 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727458 r1", "GSM6727458", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11L_IO7719-2_S6_R1_001.fastq.gz 20200117_LIB11L_IO7719-2_S6_R2_001.fastq.gz", "fastq fastq", 3331789616.0, 45024184.0, "GSM6727458 r1", "0:25 1:49", "A:946310105;C:719718901;G:749385111;T:915418300;N:957199", 25, 49, null, null, 946310105, 719718901, 749385111, 915418300, 957199, "SRX18243013", "SRS15738738", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01267, 0.86765, 0.00264, 0.03942, 0.99486, 0.90467, 0.88099, 0.69827, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72144, "SRR22266715", "SRX18243012", "SRS15738737", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "3 dpa replicate 2 scRNAseq", "GSM6727457", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "3 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "GSM6727457", "GSM6727457: 3 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727457 r1", "GSM6727457", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11K_IO7719-2_S5_R1_001.fastq.gz 20200117_LIB11K_IO7719-2_S5_R2_001.fastq.gz", "fastq fastq", 3365491954.0, 45479621.0, "GSM6727457 r1", "0:25 1:49", "A:971335843;C:704444584;G:748234229;T:940472048;N:1005250", 25, 49, null, null, 971335843, 704444584, 748234229, 940472048, 1005250, "SRX18243012", "SRS15738737", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01131, 0.8537, 0.00273, 0.04803, 0.99299, 0.85557, 0.84434, 0.68314, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72145, "SRR22266716", "SRX18243011", "SRS15738736", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "2 dpa replicate 2 scRNAseq", "GSM6727456", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "2 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "GSM6727456", "GSM6727456: 2 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727456 r1", "GSM6727456", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11J_IO7719-2_S4_R1_001.fastq.gz 20200117_LIB11J_IO7719-2_S4_R2_001.fastq.gz", "fastq fastq", 2957589524.0, 39967426.0, "GSM6727456 r1", "0:25 1:49", "A:854274479;C:615108438;G:659483480;T:827845660;N:877467", 25, 49, null, null, 854274479, 615108438, 659483480, 827845660, 877467, "SRX18243011", "SRS15738736", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01096, 0.85133, 0.00285, 0.07036, 0.99245, 0.82542, 0.82529, 0.61995, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72146, "SRR22266717", "SRX18243010", "SRS15738735", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "1 dpa replicate 2 scRNAseq", "GSM6727455", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "1 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "GSM6727455", "GSM6727455: 1 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727455 r1", "GSM6727455", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11I_IO7719-2_S3_R1_001.fastq.gz 20200117_LIB11I_IO7719-2_S3_R2_001.fastq.gz", "fastq fastq", 3092505880.0, 41790620.0, "GSM6727455 r1", "0:25 1:49", "A:895995983;C:641925155;G:682159952;T:871498883;N:925907", 25, 49, null, null, 895995983, 641925155, 682159952, 871498883, 925907, "SRX18243010", "SRS15738735", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01185, 0.82809, 0.00327, 0.07186, 0.99129, 0.84287, 0.7735, 0.60648, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72147, "SRR22266718", "SRX18243009", "SRS15738734", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "0 dpa replicate 2 scRNAseq", "GSM6727454", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "0 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "GSM6727454", "GSM6727454: 0 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727454 r1", "GSM6727454", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11H_IO7719-2_S2_R1_001.fastq.gz 20200117_LIB11H_IO7719-2_S2_R2_001.fastq.gz", "fastq fastq", 3244996940.0, 43851310.0, "GSM6727454 r1", "0:25 1:49", "A:946884027;C:670640701;G:719365748;T:907134285;N:972179", 25, 49, null, null, 946884027, 670640701, 719365748, 907134285, 972179, "SRX18243009", "SRS15738734", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01005, 0.81799, 0.00308, 0.10915, 0.99448, 0.86064, 0.79416, 0.67831, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72148, "SRR22266719", "SRX18243008", "SRS15738733", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "mock replicate 2 scRNAseq", "GSM6727453", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "mock replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "GSM6727453", "GSM6727453: mock replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727453 r1", "GSM6727453", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11G_IO7719-2_S1_R1_001.fastq.gz 20200117_LIB11G_IO7719-2_S1_R2_001.fastq.gz", "fastq fastq", 3356731834.0, 45361241.0, "GSM6727453 r1", "0:25 1:49", "A:980697276;C:699683694;G:745214776;T:930134870;N:1001218", 25, 49, null, null, 980697276, 699683694, 745214776, 930134870, 1001218, "SRX18243008", "SRS15738733", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.011, 0.79428, 0.00351, 0.11936, 0.99373, 0.85478, 0.75547, 0.68815, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72149, "SRR22266720", "SRX18243007", "SRS15738732", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "7 dpa replicate 1 scRNAseq", "GSM6727452", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "7 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "GSM6727452", "GSM6727452: 7 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727452 r1", "GSM6727452", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11F_IO7718_S6_R1_001.fastq.gz 20200107_LIB11F_IO7718_S6_R2_001.fastq.gz", "fastq fastq", 4840197106.0, 65408069.0, "GSM6727452 r1", "0:25 1:49", "A:1400160545;C:1045739437;G:1129539602;T:1263108590;N:1648932", 25, 49, null, null, 1400160545, 1045739437, 1129539602, 1263108590, 1648932, "SRX18243007", "SRS15738732", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00433, 0.87197, 0.00121, 0.03946, 0.99849, 0.89603, 0.90123, 0.67206, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72150, "SRR22266721", "SRX18243006", "SRS15738731", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "3 dpa replicate 1 scRNAseq", "GSM6727451", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "3 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "GSM6727451", "GSM6727451: 3 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727451 r1", "GSM6727451", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11E_IO7718_S5_R1_001.fastq.gz 20200107_LIB11E_IO7718_S5_R2_001.fastq.gz", "fastq fastq", 3874899962.0, 52363513.0, "GSM6727451 r1", "0:25 1:49", "A:1146498594;C:801586968;G:878214009;T:1047253303;N:1347088", 25, 49, null, null, 1146498594, 801586968, 878214009, 1047253303, 1347088, "SRX18243006", "SRS15738731", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00431, 0.83478, 0.00141, 0.0513, 0.99803, 0.84839, 0.89787, 0.68748, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72151, "SRR22266722", "SRX18243005", "SRS15738730", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "2 dpa replicate 1 scRNAseq", "GSM6727450", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "2 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "GSM6727450", "GSM6727450: 2 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727450 r1", "GSM6727450", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11D_IO7718_S4_R1_001.fastq.gz 20200107_LIB11D_IO7718_S4_R2_001.fastq.gz", "fastq fastq", 4290500982.0, 57979743.0, "GSM6727450 r1", "0:25 1:49", "A:1253875889;C:893179946;G:979642333;T:1162325902;N:1476912", 25, 49, null, null, 1253875889, 893179946, 979642333, 1162325902, 1476912, "SRX18243005", "SRS15738730", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00318, 0.85906, 0.00119, 0.07192, 0.99791, 0.81201, 0.87066, 0.6047, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72152, "SRR22266723", "SRX18243004", "SRS15738729", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "1 dpa replicate 1 scRNAseq", "GSM6727449", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "1 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "GSM6727449", "GSM6727449: 1 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727449 r1", "GSM6727449", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11C_IO7718_S3_R1_001.fastq.gz 20200107_LIB11C_IO7718_S3_R2_001.fastq.gz", "fastq fastq", 4132383258.0, 55843017.0, "GSM6727449 r1", "0:25 1:49", "A:1190680505;C:866874473;G:962110856;T:1111280875;N:1436549", 25, 49, null, null, 1190680505, 866874473, 962110856, 1111280875, 1436549, "SRX18243004", "SRS15738729", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00379, 0.84562, 0.00142, 0.07321, 0.99793, 0.82974, 0.87967, 0.60001, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72153, "SRR22266724", "SRX18243003", "SRS15738728", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "0 dpa replicate 1 scRNAseq", "GSM6727448", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "0 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "GSM6727448", "GSM6727448: 0 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727448 r1", "GSM6727448", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11B_IO7718_S2_R1_001.fastq.gz 20200107_LIB11B_IO7718_S2_R2_001.fastq.gz", "fastq fastq", 3517854180.0, 47538570.0, "GSM6727448 r1", "0:25 1:49", "A:1048135042;C:723233290;G:804794008;T:940454450;N:1237390", 25, 49, null, null, 1048135042, 723233290, 804794008, 940454450, 1237390, "SRX18243003", "SRS15738728", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00348, 0.83158, 0.00149, 0.11394, 0.99817, 0.84737, 0.77258, 0.68387, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72154, "SRR22266725", "SRX18243002", "SRS15738727", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "mock replicate 1 scRNAseq", "GSM6727447", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "mock replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "GSM6727447", "GSM6727447: mock replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727447 r1", "GSM6727447", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11A_IO7718_S1_R1_001.fastq.gz 20200107_LIB11A_IO7718_S1_R2_001.fastq.gz", "fastq fastq", 3054768766.0, 41280659.0, "GSM6727447 r1", "0:25 1:49", "A:927118702;C:625458757;G:696040428;T:805077948;N:1072931", 25, 49, null, null, 927118702, 625458757, 696040428, 805077948, 1072931, "SRX18243002", "SRS15738727", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00329, 0.78939, 0.00143, 0.12148, 0.99819, 0.84214, 0.82711, 0.67658, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72155, "SRR22266726", "SRX18243001", "SRS15738726", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured GFP+ cells replicate 1 scRNAseq", "GSM6727446", null, "source name:liver|tissue:liver|cell type:GFP+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured GFP+ cells replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:GFP+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727446", "GSM6727446: uninjured GFP+ cells replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727446 r1", "GSM6727446", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10D_IO7549_S4_R1_001.fastq.gz 20191106_LIB10D_IO7549_S4_R2_001.fastq.gz", "fastq fastq", 8587107112.0, 116041988.0, "GSM6727446 r1", "0:25 1:49", "A:2580895720;C:1753463233;G:1921984995;T:2327869497;N:2893667", 25, 49, null, null, 2580895720, 1753463233, 1921984995, 2327869497, 2893667, "SRX18243001", "SRS15738726", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02318, 0.81602, 0.00376, 0.07042, 0.99464, 0.925, 0.94019, 0.87362, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72156, "SRR22266727", "SRX18243000", "SRS15738725", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured mCherry+ cells replicate 3 scRNAseq", "GSM6727445", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured mCherry+ cells replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727445", "GSM6727445: uninjured mCherry+ cells replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727445 r1", "GSM6727445", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10C_IO7549_S3_R1_001.fastq.gz 20191106_LIB10C_IO7549_S3_R2_001.fastq.gz", "fastq fastq", 8043400252.0, 108694598.0, "GSM6727445 r1", "0:25 1:49", "A:2306379322;C:1670142146;G:1834433742;T:2229698464;N:2746578", 25, 49, null, null, 2306379322, 1670142146, 1834433742, 2229698464, 2746578, "SRX18243000", "SRS15738725", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02105, 0.77629, 0.00529, 0.12681, 0.98827, 0.84358, 0.77585, 0.67675, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72157, "SRR22266728", "SRX18242999", "SRS15738724", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured mCherry+ cells replicate 2 scRNAseq", "GSM6727444", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured mCherry+ cells replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727444", "GSM6727444: uninjured mCherry+ cells replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727444 r1", "GSM6727444", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10B_IO7549_S2_R1_001.fastq.gz 20191106_LIB10B_IO7549_S2_R2_001.fastq.gz", "fastq fastq", 7485031772.0, 101149078.0, "GSM6727444 r1", "0:25 1:49", "A:2109751380;C:1556629400;G:1728261758;T:2087832467;N:2556767", 25, 49, null, null, 2109751380, 1556629400, 1728261758, 2087832467, 2556767, "SRX18242999", "SRS15738724", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02151, 0.80489, 0.00493, 0.13325, 0.9893, 0.84776, 0.77861, 0.68035, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72158, "SRR22266729", "SRX18242998", "SRS15738723", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured mCherry+ cells replicate 1 scRNAseq", "GSM6727443", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured mCherry+ cells replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727443", "GSM6727443: uninjured mCherry+ cells replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727443 r1", "GSM6727443", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10A_IO7549_S1_R1_001.fastq.gz 20191106_LIB10A_IO7549_S1_R2_001.fastq.gz", "fastq fastq", 9329321266.0, 126071909.0, "GSM6727443 r1", "0:25 1:49", "A:2676820500;C:1936185283;G:2114138905;T:2598981203;N:3195375", 25, 49, null, null, 2676820500, 1936185283, 2114138905, 2598981203, 3195375, "SRX18242998", "SRS15738723", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01987, 0.75428, 0.00528, 0.13497, 0.98963, 0.84887, 0.73157, 0.68004, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72159, "SRR22266730", "SRX18242997", "SRS15738722", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 6 scRNAseq", "GSM6727442", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 6 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727442", "GSM6727442: uninjured replicate 6 scRNAseq; Danio rerio; RNA Seq", "GSM6727442 r1", "GSM6727442", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180316_LIB3D_IO5377-2_S3_R1_001.fastq.gz 20180316_LIB3D_IO5377-2_S3_R2_001.fastq.gz", "fastq fastq", 8019262192.0, 108368408.0, "GSM6727442 r1", "0:25 1:49", "A:2321354742;C:1785680783;G:1617017094;T:2294899508;N:310065", 25, 49, null, null, 2321354742, 1785680783, 1617017094, 2294899508, 310065, "SRX18242997", "SRS15738722", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01825, 0.43176, 0.00603, 0.0356, 0.99054, 0.93872, 0.39005, 0.39912, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72160, "SRR22266731", "SRX18242996", "SRS15738721", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 5 scRNAseq", "GSM6727441", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 5 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727441", "GSM6727441: uninjured replicate 5 scRNAseq; Danio rerio; RNA Seq", "GSM6727441 r1", "GSM6727441", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180316_LIB3C_IO5377-2_S2_R1_001.fastq.gz 20180316_LIB3C_IO5377-2_S2_R2_001.fastq.gz", "fastq fastq", 9922950894.0, 134093931.0, "GSM6727441 r1", "0:25 1:49", "A:2400612356;C:2523653639;G:2164027118;T:2834273253;N:384528", 25, 49, null, null, 2400612356, 2523653639, 2164027118, 2834273253, 384528, "SRX18242996", "SRS15738721", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01765, 0.24689, 0.00828, 0.03521, 0.9891, 0.93519, 0.74426, 0.65974, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72161, "SRR22266732", "SRX18242995", "SRS15738720", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 4 scRNAseq", "GSM6727440", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 4 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727440", "GSM6727440: uninjured replicate 4 scRNAseq; Danio rerio; RNA Seq", "GSM6727440 r1", "GSM6727440", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180316_LIB3A_IO5377-2_S1_R1_001.fastq.gz 20180316_LIB3A_IO5377-2_S1_R2_001.fastq.gz", "fastq fastq", 7562034174.0, 102189651.0, "GSM6727440 r1", "0:25 1:49", "A:2082168365;C:1773377474;G:1641155438;T:2065037229;N:295668", 25, 49, null, null, 2082168365, 1773377474, 1641155438, 2065037229, 295668, "SRX18242995", "SRS15738720", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01855, 0.34293, 0.00452, 0.03498, 0.9876, 0.94, 0.33164, 0.69274, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72162, "SRR22266733", "SRX18242994", "SRS15738719", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 3 scRNAseq", "GSM6727439", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727439", "GSM6727439: uninjured replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727439 r1", "GSM6727439", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180110_LIB2C_IO5170_S3_R1_001.fastq.gz 20180110_LIB2C_IO5170_S3_R2_001.fastq.gz", "fastq fastq", 6157056188.0, 83203462.0, "GSM6727439 r1", "0:25 1:49", "A:1886755825;C:1290134096;G:1216099330;T:1757471956;N:6594981", 25, 49, null, null, 1886755825, 1290134096, 1216099330, 1757471956, 6594981, "SRX18242994", "SRS15738719", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.0143, 0.53292, 0.0083, 0.06283, 0.99492, 0.94065, 0.83431, 0.72216, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72163, "SRR22266734", "SRX18242993", "SRS15738718", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 2 scRNAseq", "GSM6727438", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727438", "GSM6727438: uninjured replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727438 r1", "GSM6727438", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180110_LIB2B_IO5170_S2_R1_001.fastq.gz 20180110_LIB2B_IO5170_S2_R2_001.fastq.gz", "fastq fastq", 4085425374.0, 55208451.0, "GSM6727438 r1", "0:25 1:49", "A:1148951414;C:943475846;G:839192575;T:1149676508;N:4129031", 25, 49, null, null, 1148951414, 943475846, 839192575, 1149676508, 4129031, "SRX18242993", "SRS15738718", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01678, 0.38499, 0.00747, 0.03999, 0.99299, 0.95298, 0.82687, 0.74374, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72164, "SRR22266735", "SRX18242992", "SRS15738717", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 1 scRNAseq", "GSM6727437", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727437", "GSM6727437: uninjured replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727437 r1", "GSM6727437", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180110_LIB2A_IO5170_S1_R1_001.fastq.gz 20180110_LIB2A_IO5170_S1_R2_001.fastq.gz", "fastq fastq", 5454978746.0, 73715929.0, "GSM6727437 r1", "0:25 1:49", "A:1662394748;C:1166773893;G:1080027941;T:1540187839;N:5594325", 25, 49, null, null, 1662394748, 1166773893, 1080027941, 1540187839, 5594325, "SRX18242992", "SRS15738717", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02089, 0.45353, 0.01367, 0.0687, 0.99168, 0.93139, 0.76523, 0.68002, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [74105, "SRR23380800", "SRX19321399", "SRS16719697", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 50% epiboly NT replicate B scRNAseq", "GSM7035744", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo 50% epiboly NT replicate B scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT", "GSM7035744", "GSM7035744: zebrafish embryo 50% epiboly NT replicate B scRNAseq; Danio rerio; RNA Seq", "GSM7035744 r1", "GSM7035744", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B09_S9_I1_001.fastq.gz B09_S9_R1_001.fastq.gz B09_S9_R2_001.fastq.gz", "fastq fastq fastq", 1731750720.0, 10308040.0, "GSM7035744 r1", "0:8 1:20 2:140", "A:483160966;C:257831212;G:374014730;T:328009839;N:108853", 8, 20, 140, null, 483160966, 257831212, 374014730, 328009839, 108853, "SRX19321399", "SRS16719697", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.76439, null, 0.04865, null, 0.85794, null, 0.69865, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74106, "SRR23380801", "SRX19321398", "SRS16719698", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 50% epiboly IAA replicate B scRNAseq", "GSM7035743", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo 50% epiboly IAA replicate B scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA", "GSM7035743", "GSM7035743: zebrafish embryo 50% epiboly IAA replicate B scRNAseq; Danio rerio; RNA Seq", "GSM7035743 r1", "GSM7035743", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B10_S10_I1_001.fastq.gz B10_S10_R1_001.fastq.gz B10_S10_R2_001.fastq.gz", "fastq fastq fastq", 1449614208.0, 8628656.0, "GSM7035743 r1", "0:8 1:20 2:140", "A:383054921;C:231791450;G:292787007;T:300288679;N:89783", 8, 20, 140, null, 383054921, 231791450, 292787007, 300288679, 89783, "SRX19321398", "SRS16719698", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.69705, null, 0.03055, null, 0.86009, null, 0.49815, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74107, "SRR23380802", "SRX19321397", "SRS16719696", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 50% epiboly NT replicate A scRNAseq", "GSM7035742", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo 50% epiboly NT replicate A scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT", "GSM7035742", "GSM7035742: zebrafish embryo 50% epiboly NT replicate A scRNAseq; Danio rerio; RNA Seq", "GSM7035742 r1", "GSM7035742", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B03_S3_I1_001.fastq.gz B03_S3_R1_001.fastq.gz B03_S3_R2_001.fastq.gz", "fastq fastq fastq", 3289212696.0, 19578647.0, "GSM7035742 r1", "0:8 1:20 2:140", "A:917014925;C:511489537;G:636621002;T:675689845;N:195271", 8, 20, 140, null, 917014925, 511489537, 636621002, 675689845, 195271, "SRX19321397", "SRS16719696", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.84983, null, 0.0403, null, 0.84948, null, 0.66672, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74108, "SRR23380803", "SRX19321396", "SRS16719695", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 50% epiboly IAA replicate A scRNAseq", "GSM7035741", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo 50% epiboly IAA replicate A scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA", "GSM7035741", "GSM7035741: zebrafish embryo 50% epiboly IAA replicate A scRNAseq; Danio rerio; RNA Seq", "GSM7035741 r1", "GSM7035741", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B04_S4_R1_001.fastq.gz B04_S4_R2_001.fastq.gz B04_S4_I1_001.fastq.gz", "fastq fastq fastq", 18799793040.0, 111903530.0, "GSM7035741 r1", "0:8 1:20 2:140", "A:5320607436;C:2779767285;G:3920270375;T:3644700536;N:1148568", 8, 20, 140, null, 5320607436, 2779767285, 3920270375, 3644700536, 1148568, "SRX19321396", "SRS16719695", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.64644, null, 0.0354, null, 0.85886, null, 0.48293, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74109, "SRR23380804", "SRX19321395", "SRS16719694", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo zfs:0000015 NT replicate B scRNAseq", "GSM7035740", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo zfs:0000015 NT replicate B scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT", "GSM7035740", "GSM7035740: zebrafish embryo zfs:0000015 NT replicate B scRNAseq; Danio rerio; RNA Seq", "GSM7035740 r1", "GSM7035740", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B07_S7_I1_001.fastq.gz B07_S7_R1_001.fastq.gz B07_S7_R2_001.fastq.gz", "fastq fastq fastq", 5107507608.0, 30401831.0, "GSM7035740 r1", "0:8 1:20 2:140", "A:1271612661;C:768251429;G:1315055363;T:901018360;N:318527", 8, 20, 140, null, 1271612661, 768251429, 1315055363, 901018360, 318527, "SRX19321395", "SRS16719694", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.6633, null, 0.0322, null, 0.86898, null, 0.73112, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74110, "SRR23380805", "SRX19321394", "SRS16719693", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo zfs:0000015 IAA replicate B scRNAseq", "GSM7035739", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo zfs:0000015 IAA replicate B scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA", "GSM7035739", "GSM7035739: zebrafish embryo zfs:0000015 IAA replicate B scRNAseq; Danio rerio; RNA Seq", "GSM7035739 r1", "GSM7035739", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B08_S8_R2_001.fastq.gz B08_S8_R1_001.fastq.gz B08_S8_I1_001.fastq.gz", "fastq fastq fastq", 6618266424.0, 39394443.0, "GSM7035739 r1", "0:8 1:20 2:140", "A:1772472371;C:1058335373;G:1382074511;T:1301941080;N:398685", 8, 20, 140, null, 1772472371, 1058335373, 1382074511, 1301941080, 398685, "SRX19321394", "SRS16719693", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.66052, null, 0.03428, null, 0.84902, null, 0.4999, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74111, "SRR23380806", "SRX19321393", "SRS16719692", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo zfs:0000015 NT replicate A scRNAseq", "GSM7035738", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo zfs:0000015 NT replicate A scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT", "GSM7035738", "GSM7035738: zebrafish embryo zfs:0000015 NT replicate A scRNAseq; Danio rerio; RNA Seq", "GSM7035738 r1", "GSM7035738", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. 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We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo zfs:0000015 IAA replicate A scRNAseq", "GSM7035737", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo zfs:0000015 IAA replicate A scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA", "GSM7035737", "GSM7035737: zebrafish embryo zfs:0000015 IAA replicate A scRNAseq; Danio rerio; RNA Seq", "GSM7035737 r1", "GSM7035737", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. 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This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo Dome NT replicate B scRNAseq", "GSM7035736", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo Dome NT replicate B scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:NT", "GSM7035736", "GSM7035736: zebrafish embryo Dome NT replicate B scRNAseq; Danio rerio; RNA Seq", "GSM7035736 r1", "GSM7035736", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B05_S5_I1_001.fastq.gz B05_S5_R1_001.fastq.gz B05_S5_R2_001.fastq.gz", "fastq fastq fastq", 8803995984.0, 52404738.0, "GSM7035736 r1", "0:8 1:20 2:140", "A:2610393348;C:1221729748;G:1971221134;T:1532772530;N:546560", 8, 20, 140, null, 2610393348, 1221729748, 1971221134, 1532772530, 546560, "SRX19321391", "SRS16719689", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.6884, null, 0.03585, null, 0.86423, null, 0.72819, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74114, "SRR23380809", "SRX19321390", "SRS16719690", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell SLAM seq 3 developmental stages with treated and untreated samples and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo Dome IAA replicate B scRNAseq", "GSM7035735", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo Dome IAA replicate B scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al. Science 2018 using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:IAA", "GSM7035735", "GSM7035735: zebrafish embryo Dome IAA replicate B scRNAseq; Danio rerio; RNA Seq", "GSM7035735 r1", "GSM7035735", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015 available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8 and incubated in IAA solution 50mM NaPO4 pH8 10mM IAA 20% DMSO 6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction and 12\u201313 cycles of PCR amplification were performed. 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