{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and technology = \"dropseq\"", "rows": [[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. 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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 . 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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 . 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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"]], "truncated": false, 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"run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", 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