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38 rows where experiment.platform = "ILLUMINA", technology = "dropseq" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation 4

experiment.library_source 2

tissue_curation_coarse 1

  • All anatomical structures · 38 ✖

tissue_curation 1

technology 1

  • dropseq · 38 ✖

experiment.platform 1

  • ILLUMINA · 38 ✖

experiment.library_strategy 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
44502 44502 SRR6261604 SRX3367886 SRS2665528 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo shield Rep 1 GSM2838533   tissue:Wild type TLAB Embryo|developmental stage:shield|hpf batch:DS5 WT zebrafish embryo shield Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:shield|hpf batch:DS5 GSM2838533 GSM2838533: WT zebrafish embryo shield Rep 1; Danio rerio; RNA Seq GSM2838533   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838533 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFS-DS5.bam bam 3179843792.0 55979578.0 GSM2838533 r1 0:56.80 A:961841501;C:638551921;G:690013778;T:888532131;N:904461 56       961841501 638551921 690013778 888532131 904461 SRX3367886 SRS2665528 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90259   0.05737   0.88183   0.63826   39   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44503 44503 SRR6261603 SRX3367885 SRS2665527 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo oblong Rep 2 GSM2838532   tissue:Wild type TLAB Embryo|developmental stage:oblong|hpf batch:DS5 WT zebrafish embryo oblong Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:oblong|hpf batch:DS5 GSM2838532 GSM2838532: WT zebrafish embryo oblong Rep 2; Danio rerio; RNA Seq GSM2838532   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838532 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFOBLONG-DS5b.bam bam 196960038.0 3732948.0 GSM2838532 r1 0:52.76 A:59884724;C:41040872;G:44343848;T:51548840;N:141754 52       59884724 41040872 44343848 51548840 141754 SRX3367885 SRS2665527 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.9008   0.0487   0.83333   0.69396   26   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Blastula Embryo Embryo Imprecise All anatomical structures
44504 44504 SRR6261602 SRX3367884 SRS2665526 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo oblong Rep 1 GSM2838531   tissue:Wild type TLAB Embryo|developmental stage:oblong|hpf batch:DS5 WT zebrafish embryo oblong Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:oblong|hpf batch:DS5 GSM2838531 GSM2838531: WT zebrafish embryo oblong Rep 1; Danio rerio; RNA Seq GSM2838531   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838531 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFOBLONG-DS5.bam bam 4345336162.0 73291146.0 GSM2838531 r1 0:59.29 A:1334141601;C:893306177;G:989357821;T:1127952860;N:577703 59       1334141601 893306177 989357821 1127952860 577703 SRX3367884 SRS2665526 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.88987   0.04135   0.88444   0.69674   30   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Blastula Embryo Embryo Imprecise All anatomical structures
44505 44505 SRR6261601 SRX3367883 SRS2665524 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo high Rep 2 GSM2838530   tissue:Wild type TLAB Embryo|developmental stage:high|hpf batch:DS5 WT zebrafish embryo high Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:high|hpf batch:DS5 GSM2838530 GSM2838530: WT zebrafish embryo high Rep 2; Danio rerio; RNA Seq GSM2838530   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFHIGH-DS5b.bam bam 737038001.0 12994158.0 GSM2838530 r1 0:56.72 A:222013994;C:149289044;G:161706547;T:203898449;N:129967 56       222013994 149289044 161706547 203898449 129967 SRX3367883 SRS2665524 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.82793   0.04496   0.82593   0.64576   37   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Undetermined Embryo Embryo Imprecise All anatomical structures
44506 44506 SRR6261600 SRX3367882 SRS2665523 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo high Rep 1 GSM2838529   tissue:Wild type TLAB Embryo|developmental stage:high|hpf batch:DS5 WT zebrafish embryo high Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:high|hpf batch:DS5 GSM2838529 GSM2838529: WT zebrafish embryo high Rep 1; Danio rerio; RNA Seq GSM2838529   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838529 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFHIGH-DS5.bam bam 1150193271.0 19592509.0 GSM2838529 r1 0:58.71 A:355328611;C:231282565;G:256994557;T:306435407;N:152131 58       355328611 231282565 256994557 306435407 152131 SRX3367882 SRS2665523 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.88537   0.04181   0.87371   0.67546   62   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Undetermined Embryo Embryo Imprecise All anatomical structures
44507 44507 SRR6261599 SRX3367881 SRS2665525 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo dome Rep 1 GSM2838528   tissue:Wild type TLAB Embryo|developmental stage:dome|hpf batch:DS5 WT zebrafish embryo dome Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:dome|hpf batch:DS5 GSM2838528 GSM2838528: WT zebrafish embryo dome Rep 1; Danio rerio; RNA Seq GSM2838528   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838528 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFDOME-DS5.bam bam 2986150374.0 51431163.0 GSM2838528 r1 0:58.06 A:917833789;C:596671084;G:649280401;T:821959372;N:405728 58       917833789 596671084 649280401 821959372 405728 SRX3367881 SRS2665525 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.87678   0.05628   0.88937   0.37085   44   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Blastula Embryo Embryo Imprecise All anatomical structures
44508 44508 SRR6261598 SRX3367880 SRS2665522 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo bud Rep 4 GSM2838527   tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS4 WT zebrafish embryo bud Rep 4 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:bud|hpf batch:DS4 GSM2838527 GSM2838527: WT zebrafish embryo bud Rep 4; Danio rerio; RNA Seq GSM2838527   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838527 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFB-DS4.bam bam 6450238418.0 135245227.0 GSM2838527 r1 0:47.69 A:1923004447;C:1355829109;G:1430733445;T:1734702312;N:5969105 47       1923004447 1355829109 1430733445 1734702312 5969105 SRX3367880 SRS2665522 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.88781   0.09347   0.84358   0.63177   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Undetermined Embryo Embryo Imprecise All anatomical structures
44509 44509 SRR6261597 SRX3367879 SRS2665521 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo bud Rep 3 GSM2838526   tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS3 WT zebrafish embryo bud Rep 3 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:bud|hpf batch:DS3 GSM2838526 GSM2838526: WT zebrafish embryo bud Rep 3; Danio rerio; RNA Seq GSM2838526   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838526 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFB-DS3.bam bam 12589500684.0 264160754.0 GSM2838526 r1 0:47.66 A:3735824308;C:2614320755;G:2828705000;T:3402591139;N:8059482 47       3735824308 2614320755 2828705000 3402591139 8059482 SRX3367879 SRS2665521 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90065   0.08373   0.82716   0.64737   39   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Undetermined Embryo Embryo Imprecise All anatomical structures
44510 44510 SRR6261596 SRX3367878 SRS2665520 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo bud Rep 2 GSM2838525   tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS2 WT zebrafish embryo bud Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:bud|hpf batch:DS2 GSM2838525 GSM2838525: WT zebrafish embryo bud Rep 2; Danio rerio; RNA Seq GSM2838525   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838525 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFB-DS2b.bam bam 3922868275.0 82034280.0 GSM2838525 r1 0:47.82 A:1201317525;C:820872807;G:873362887;T:1027226159;N:88897 47       1201317525 820872807 873362887 1027226159 88897 SRX3367878 SRS2665520 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.91489   0.07264   0.84684   0.68127   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Undetermined Embryo Embryo Imprecise All anatomical structures
44511 44511 SRR6261595 SRX3367877 SRS2665519 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo bud Rep 1 GSM2838524   tissue:Wild type TLAB Embryo|developmental stage:bud|hpf batch:DS2 WT zebrafish embryo bud Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:bud|hpf batch:DS2 GSM2838524 GSM2838524: WT zebrafish embryo bud Rep 1; Danio rerio; RNA Seq GSM2838524   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838524 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZFB-DS2.bam bam 1962943074.0 40871825.0 GSM2838524 r1 0:48.03 A:591046898;C:412519355;G:441566116;T:516943702;N:867003 48       591046898 412519355 441566116 516943702 867003 SRX3367877 SRS2665519 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.91352   0.10693   0.82921   0.62781   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Undetermined Embryo Embryo Imprecise All anatomical structures
44512 44512 SRR6261594 SRX3367876 SRS2665517 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 90% epiboly Rep 3 GSM2838523   tissue:Wild type TLAB Embryo|developmental stage:90% epiboly|hpf batch:DS4 WT zebrafish embryo 90% epiboly Rep 3 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:90% epiboly|hpf batch:DS4 GSM2838523 GSM2838523: WT zebrafish embryo 90% epiboly Rep 3; Danio rerio; RNA Seq GSM2838523   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838523 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF90-DS4.bam bam 4842842267.0 101293760.0 GSM2838523 r1 0:47.81 A:1463148609;C:1002649035;G:1087078720;T:1284643937;N:5321966 47       1463148609 1002649035 1087078720 1284643937 5321966 SRX3367876 SRS2665517 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90073   0.07593   0.85656   0.66721   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44513 44513 SRR6261593 SRX3367875 SRS2665518 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 90% epiboly Rep 2 GSM2838522   tissue:Wild type TLAB Embryo|developmental stage:90% epiboly|hpf batch:DS3 WT zebrafish embryo 90% epiboly Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:90% epiboly|hpf batch:DS3 GSM2838522 GSM2838522: WT zebrafish embryo 90% epiboly Rep 2; Danio rerio; RNA Seq GSM2838522   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838522 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF90-DS3.bam bam 5932111443.0 123808277.0 GSM2838522 r1 0:47.91 A:1786246386;C:1223369366;G:1319845082;T:1598104737;N:4545872 47       1786246386 1223369366 1319845082 1598104737 4545872 SRX3367875 SRS2665518 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90983   0.07417   0.84887   0.69062   41   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44514 44514 SRR6261592 SRX3367874 SRS2665514 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 90% epiboly Rep 1 GSM2838521   tissue:Wild type TLAB Embryo|developmental stage:90% epiboly|hpf batch:DS2 WT zebrafish embryo 90% epiboly Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:90% epiboly|hpf batch:DS2 GSM2838521 GSM2838521: WT zebrafish embryo 90% epiboly Rep 1; Danio rerio; RNA Seq GSM2838521   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838521 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF90-DS2.bam bam 9413100575.0 196594599.0 GSM2838521 r1 0:47.88 A:2915813449;C:1944788007;G:2074752689;T:2470632938;N:7113492 47       2915813449 1944788007 2074752689 2470632938 7113492 SRX3367874 SRS2665514 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90701   0.09183   0.84997   0.70905   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44515 44515 SRR6261591 SRX3367873 SRS2665516 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 75% epiboly Rep 3 GSM2838520   tissue:Wild type TLAB Embryo|developmental stage:75% epiboly|hpf batch:DS4 WT zebrafish embryo 75% epiboly Rep 3 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:75% epiboly|hpf batch:DS4 GSM2838520 GSM2838520: WT zebrafish embryo 75% epiboly Rep 3; Danio rerio; RNA Seq GSM2838520   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838520 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF75-DS4.bam bam 3915590024.0 82098818.0 GSM2838520 r1 0:47.69 A:1146132665;C:796349091;G:856725624;T:1112518655;N:3863989 47       1146132665 796349091 856725624 1112518655 3863989 SRX3367873 SRS2665516 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.89527   0.06395   0.85395   0.61881   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44516 44516 SRR6261590 SRX3367872 SRS2665513 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 75% epiboly Rep 2 GSM2838519   tissue:Wild type TLAB Embryo|developmental stage:75% epiboly|hpf batch:DS3 WT zebrafish embryo 75% epiboly Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:75% epiboly|hpf batch:DS3 GSM2838519 GSM2838519: WT zebrafish embryo 75% epiboly Rep 2; Danio rerio; RNA Seq GSM2838519   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838519 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF75-DS3.bam bam 6260674990.0 130686591.0 GSM2838519 r1 0:47.91 A:1860503244;C:1298121538;G:1397241096;T:1699896990;N:4912122 47       1860503244 1298121538 1397241096 1699896990 4912122 SRX3367872 SRS2665513 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90879   0.05607   0.849   0.64494   34   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44517 44517 SRR6261589 SRX3367871 SRS2665512 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 75% epiboly Rep 1 GSM2838518   tissue:Wild type TLAB Embryo|developmental stage:75% epiboly|hpf batch:DS2 WT zebrafish embryo 75% epiboly Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:75% epiboly|hpf batch:DS2 GSM2838518 GSM2838518: WT zebrafish embryo 75% epiboly Rep 1; Danio rerio; RNA Seq GSM2838518   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838518 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF75-DS2.bam bam 12515631279.0 259899014.0 GSM2838518 r1 0:48.16 A:3844536415;C:2601284821;G:2774529684;T:3284967732;N:10312627 48       3844536415 2601284821 2774529684 3284967732 10312627 SRX3367871 SRS2665512 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.91618   0.08367   0.85695   0.69056   19   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44518 44518 SRR6261588 SRX3367870 SRS2665511 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 6 somite Rep 2 GSM2838517   tissue:Wild type TLAB Embryo|developmental stage:6 somite|hpf batch:DS5 WT zebrafish embryo 6 somite Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:6 somite|hpf batch:DS5 GSM2838517 GSM2838517: WT zebrafish embryo 6 somite Rep 2; Danio rerio; RNA Seq GSM2838517   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838517 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF6S-DS5b.bam bam 5483131316.0 97533075.0 GSM2838517 r1 0:56.22 A:1682994930;C:1124480753;G:1213976098;T:1459811169;N:1868366 56       1682994930 1124480753 1213976098 1459811169 1868366 SRX3367870 SRS2665511 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.89126   0.1186   0.85476   0.62994   62   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Segmentation Embryo Embryo Imprecise All anatomical structures
44519 44519 SRR6261587 SRX3367869 SRS2665510 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 6 somite Rep 1 GSM2838516   tissue:Wild type TLAB Embryo|developmental stage:6 somite|hpf batch:DS5 WT zebrafish embryo 6 somite Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:6 somite|hpf batch:DS5 GSM2838516 GSM2838516: WT zebrafish embryo 6 somite Rep 1; Danio rerio; RNA Seq GSM2838516   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF6S-DS5.bam bam 6770179128.0 120219927.0 GSM2838516 r1 0:56.31 A:2045470046;C:1445282146;G:1551331939;T:1725694334;N:2400663 56       2045470046 1445282146 1551331939 1725694334 2400663 SRX3367869 SRS2665510 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90931   0.06771   0.88306   0.62745   62   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Segmentation Embryo Embryo Imprecise All anatomical structures
44520 44520 SRR6261586 SRX3367868 SRS2665515 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 60% epiboly Rep 3 GSM2838515   tissue:Wild type TLAB Embryo|developmental stage:60% epiboly|hpf batch:DS4 WT zebrafish embryo 60% epiboly Rep 3 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:60% epiboly|hpf batch:DS4 GSM2838515 GSM2838515: WT zebrafish embryo 60% epiboly Rep 3; Danio rerio; RNA Seq GSM2838515   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF60-DS4.bam bam 3833885676.0 80339895.0 GSM2838515 r1 0:47.72 A:1148249585;C:778428304;G:832463962;T:1070132046;N:4611779 47       1148249585 778428304 832463962 1070132046 4611779 SRX3367868 SRS2665515 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.89639   0.05633   0.87184   0.71167   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44521 44521 SRR6261585 SRX3367867 SRS2665509 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 60% epiboly Rep 2 GSM2838514   tissue:Wild type TLAB Embryo|developmental stage:60% epiboly|hpf batch:DS3 WT zebrafish embryo 60% epiboly Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:60% epiboly|hpf batch:DS3 GSM2838514 GSM2838514: WT zebrafish embryo 60% epiboly Rep 2; Danio rerio; RNA Seq GSM2838514   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838514 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF60-DS3.bam bam 3811502382.0 80015031.0 GSM2838514 r1 0:47.63 A:1131311970;C:778039231;G:843841278;T:1054333041;N:3976862 47       1131311970 778039231 843841278 1054333041 3976862 SRX3367867 SRS2665509 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.8997   0.05901   0.85271   0.66877   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44522 44522 SRR6261584 SRX3367866 SRS2665508 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 60% epiboly Rep 1 GSM2838513   tissue:Wild type TLAB Embryo|developmental stage:60% epiboly|hpf batch:DS2 WT zebrafish embryo 60% epiboly Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:60% epiboly|hpf batch:DS2 GSM2838513 GSM2838513: WT zebrafish embryo 60% epiboly Rep 1; Danio rerio; RNA Seq GSM2838513   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838513 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF60-DS2.bam bam 9427367847.0 197041685.0 GSM2838513 r1 0:47.84 A:2840380863;C:1954270941;G:2115387210;T:2512438103;N:4890730 47       2840380863 1954270941 2115387210 2512438103 4890730 SRX3367866 SRS2665508 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90013   0.10453   0.84609   0.67284   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44523 44523 SRR6261583 SRX3367865 SRS2665505 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 50% epiboly Rep 4 GSM2838512   tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS4 WT zebrafish embryo 50% epiboly Rep 4 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:50% epiboly|hpf batch:DS4 GSM2838512 GSM2838512: WT zebrafish embryo 50% epiboly Rep 4; Danio rerio; RNA Seq GSM2838512   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838512 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF50-DS4b.bam bam 4244398214.0 89440689.0 GSM2838512 r1 0:47.45 A:1237706491;C:863592991;G:927386153;T:1211073503;N:4639076 47       1237706491 863592991 927386153 1211073503 4639076 SRX3367865 SRS2665505 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.87107   0.04987   0.85255   0.64831   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44524 44524 SRR6261582 SRX3367864 SRS2665503 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 50% epiboly Rep 3 GSM2838511   tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS4 WT zebrafish embryo 50% epiboly Rep 3 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:50% epiboly|hpf batch:DS4 GSM2838511 GSM2838511: WT zebrafish embryo 50% epiboly Rep 3; Danio rerio; RNA Seq GSM2838511   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838511 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF50-DS4.bam bam 4278209039.0 89476992.0 GSM2838511 r1 0:47.81 A:1290955423;C:877486318;G:942860908;T:1162275878;N:4630512 47       1290955423 877486318 942860908 1162275878 4630512 SRX3367864 SRS2665503 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.88164   0.04985   0.85522   0.68333   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44525 44525 SRR6261581 SRX3367863 SRS2665507 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 50% epiboly Rep 2 GSM2838510   tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS3 WT zebrafish embryo 50% epiboly Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:50% epiboly|hpf batch:DS3 GSM2838510 GSM2838510: WT zebrafish embryo 50% epiboly Rep 2; Danio rerio; RNA Seq GSM2838510   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838510 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF50-DS3.bam bam 3501884831.0 73345396.0 GSM2838510 r1 0:47.75 A:1070153581;C:717648649;G:775104021;T:935318712;N:3659868 47       1070153581 717648649 775104021 935318712 3659868 SRX3367863 SRS2665507 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.89876   0.05026   0.85839   0.7398   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44526 44526 SRR6261580 SRX3367862 SRS2665506 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 50% epiboly Rep 1 GSM2838509   tissue:Wild type TLAB Embryo|developmental stage:50% epiboly|hpf batch:DS2 WT zebrafish embryo 50% epiboly Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:50% epiboly|hpf batch:DS2 GSM2838509 GSM2838509: WT zebrafish embryo 50% epiboly Rep 1; Danio rerio; RNA Seq GSM2838509   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838509 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF50-DS2.bam bam 8692779007.0 181078327.0 GSM2838509 r1 0:48.01 A:2652144410;C:1801595414;G:1947473372;T:2284385129;N:7180682 48       2652144410 1801595414 1947473372 2284385129 7180682 SRX3367862 SRS2665506 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.91106   0.07336   0.8356   0.67412   50   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Gastrula Embryo Embryo Imprecise All anatomical structures
44527 44527 SRR6261579 SRX3367861 SRS2665502 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo 3 somite Rep 1 GSM2838508   tissue:Wild type TLAB Embryo|developmental stage:3 somite|hpf batch:DS5 WT zebrafish embryo 3 somite Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:3 somite|hpf batch:DS5 GSM2838508 GSM2838508: WT zebrafish embryo 3 somite Rep 1; Danio rerio; RNA Seq GSM2838508   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838508 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF3S-DS5.bam bam 4322271397.0 76613226.0 GSM2838508 r1 0:56.42 A:1302285155;C:910804445;G:1019986862;T:1087802148;N:1392787 56       1302285155 910804445 1019986862 1087802148 1392787 SRX3367861 SRS2665502 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.88196   0.09807   0.89585   0.68342   62   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Segmentation Embryo Embryo Imprecise All anatomical structures
44528 44528 SRR6261578 SRX3367860 SRS2665504 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo zfs:0000015 Rep 2 GSM2838507   tissue:Wild type TLAB Embryo|developmental stage:zfs:0000015|hpf batch:DS5 WT zebrafish embryo zfs:0000015 Rep 2 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:zfs:0000015|hpf batch:DS5 GSM2838507 GSM2838507: WT zebrafish embryo zfs:0000015 Rep 2; Danio rerio; RNA Seq GSM2838507   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838507 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF30-DS5b.bam bam 1427320072.0 27100581.0 GSM2838507 r1 0:52.67 A:430563775;C:297250590;G:322830484;T:375658913;N:1016310 52       430563775 297250590 322830484 375658913 1016310 SRX3367860 SRS2665504 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.89678   0.06492   0.85403   0.67064   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Blastula Embryo Embryo Imprecise All anatomical structures
44529 44529 SRR6261577 SRX3367859 SRS2665539 SRP124289 PRJNA417290 Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints GSE106474 Transcriptome Analysis Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. parent bioproject:PRJNA417291 pubmed:29700225   WT zebrafish embryo zfs:0000015 Rep 1 GSM2838506   tissue:Wild type TLAB Embryo|developmental stage:zfs:0000015|hpf batch:DS5 WT zebrafish embryo zfs:0000015 Rep 1 Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts Wild type TLAB Embryo   Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. developmental stage:zfs:0000015|hpf batch:DS5 GSM2838506 GSM2838506: WT zebrafish embryo zfs:0000015 Rep 1; Danio rerio; RNA Seq GSM2838506   1 Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. GEO Accession:GSM2838506 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP124289   dangling references:treat as unmapped ZF30-DS5.bam bam 1506806977.0 25842795.0 GSM2838506 r1 0:58.31 A:477897847;C:307865773;G:330036592;T:390748777;N:257988 58       477897847 307865773 330036592 390748777 257988 SRX3367859 SRS2665539 SRA628740 GEO Schier Lab, Molecular and Cellular Biology, Harvard University 1 0.90526   0.05376   0.8644   0.75191   43   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   United States 2017-11-02 Blastula Embryo Embryo Imprecise All anatomical structures
74105 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   zebrafish embryo 50% epiboly NT replicate B scRNAseq GSM7035744   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   483160966 257831212 374014730 328009839 108853 SRX19321399 SRS16719697 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.76439   0.04865   0.85794   0.69865   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Gastrula Embryo Embryo Imprecise All anatomical structures
74106 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   zebrafish embryo 50% epiboly IAA replicate B scRNAseq GSM7035743   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   383054921 231791450 292787007 300288679 89783 SRX19321398 SRS16719698 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.69705   0.03055   0.86009   0.49815   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Gastrula Embryo Embryo Imprecise All anatomical structures
74107 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   zebrafish embryo 50% epiboly NT replicate A scRNAseq GSM7035742   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   917014925 511489537 636621002 675689845 195271 SRX19321397 SRS16719696 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.84983   0.0403   0.84948   0.66672   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Gastrula Embryo Embryo Imprecise All anatomical structures
74108 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   zebrafish embryo 50% epiboly IAA replicate A scRNAseq GSM7035741   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   5320607436 2779767285 3920270375 3644700536 1148568 SRX19321396 SRS16719695 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.64644   0.0354   0.85886   0.48293   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Gastrula Embryo Embryo Imprecise All anatomical structures
74109 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   zebrafish embryo zfs:0000015 NT replicate B scRNAseq GSM7035740   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   1271612661 768251429 1315055363 901018360 318527 SRX19321395 SRS16719694 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.6633   0.0322   0.86898   0.73112   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Blastula Embryo Embryo Imprecise All anatomical structures
74110 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   zebrafish embryo zfs:0000015 IAA replicate B scRNAseq GSM7035739   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   1772472371 1058335373 1382074511 1301941080 398685 SRX19321394 SRS16719693 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.66052   0.03428   0.84902   0.4999   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Blastula Embryo Embryo Imprecise All anatomical structures
74111 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   zebrafish embryo zfs:0000015 NT replicate A scRNAseq GSM7035738   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   loader:fastq load.py B01_S1_I1_001.fastq.gz B01_S1_R1_001.fastq.gz B01_S1_R2_001.fastq.gz fastq fastq fastq 2465114064.0 14673298.0 GSM7035738 r1 0:8 1:20 2:140 A:682033408;C:384987859;G:496372763;T:490717526;N:150164 8 20 140   682033408 384987859 496372763 490717526 150164 SRX19321393 SRS16719692 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.83566   0.03718   0.85021   0.68773   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Blastula Embryo Embryo Imprecise All anatomical structures
74112 74112 SRR23380807 SRX19321392 SRS16719691 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   zebrafish embryo zfs:0000015 IAA replicate A scRNAseq GSM7035737   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   loader:fastq load.py B02_S2_I1_001.fastq.gz B02_S2_R1_001.fastq.gz B02_S2_R2_001.fastq.gz fastq fastq fastq 12337001376.0 73434532.0 GSM7035737 r1 0:8 1:20 2:140 A:3313181087;C:1943751072;G:2424458605;T:2598692748;N:750968 8 20 140   3313181087 1943751072 2424458605 2598692748 750968 SRX19321392 SRS16719691 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.73328   0.03858   0.84045   0.49156   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Blastula Embryo Embryo Imprecise All anatomical structures
74113 74113 SRR23380808 SRX19321391 SRS16719689 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   zebrafish embryo Dome NT replicate B scRNAseq GSM7035736   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   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   2610393348 1221729748 1971221134 1532772530 546560 SRX19321391 SRS16719689 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.6884   0.03585   0.86423   0.72819   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Blastula Embryo Embryo Imprecise All anatomical structures
74114 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   zebrafish embryo Dome IAA replicate B scRNAseq GSM7035735   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP422528   loader:fastq load.py B06_S6_I1_001.fastq.gz B06_S6_R1_001.fastq.gz B06_S6_R2_001.fastq.gz fastq fastq fastq 21140863800.0 125838475.0 GSM7035735 r1 0:8 1:20 2:140 A:6033328114;C:2907546987;G:4997520100;T:3677695966;N:1295333 8 20 140   6033328114 2907546987 4997520100 3677695966 1295333 SRX19321390 SRS16719690 SRA1590430 Hebrew University of Jerusalem Hebrew University of Jerusalem 1 0.54964   0.01991   0.86539   0.48683   140   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet dropseq   Israel 2023-02-09 Blastula Embryo Embryo Imprecise All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;