{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"scslamseq\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[61426, "SRR12749593", "SRX9221550", "SRS7455251", "SRP285948", "PRJNA666689", "Spatio temporal mRNA tracking in the early zebrafish embryo", "GSE158849", "Other", "We performed spatially resolved transcriptomics with sub single cell resolution in zebrafish embryos at the one cell stage  which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac  the vegetal pole. The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes  but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys  mature X. laevis and X. tropicalis oocytes. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf.", null, "pubmed:34099733", null, "tomo seq zebrafish replicate3", "GSM4812177", null, "tissue:1 cell stage embryo|strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen  cryo secti1d embryo.", "tomo seq zebrafish replicate3", "zebrafish tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode Genome build: GRCz10   release 90 Supplementary files format and content: csv file containing gene counts per section xenopus tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode and translate gene identifier to gene names Genome build: X. tropicalis v9.1 genome assembly  X.laevis v9.2 genome assembly Supplementary files format and content: csv file containing gene counts per section scSLAM seq zebrafish demultiplexing using cellranger mkfastq v3.0.2 mapping and whitelisting of cells with cellranger v3.0.2 splitting labeled reads >1 T C mutation from unlabeled into separate fastq files submitted to this GEO entry mapping with STARsolo v2.7.0f 0328 single cell analysis in seurat v3.1.2 Genome build: GRCz11 Supplementary files format and content:  barcodes.tsv list of barcodes   genes.tsv list of genes  and  matrix.tsv count matrix", "one cell stage embryo", null, "none provided by the submitter", null, "strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen  cryo secti1d embryo.", "GSM4812177", "GSM4812177: tomo seq zebrafish replicate3; Danio rerio; RNA Seq", "GSM4812177", null, "1", "none provided by the submitter", "GEO Accession:GSM4812177", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP285948", null, null, "tomoseq.zebrafish.rep3.R1.fastq.gz tomoseq.zebrafish.rep3.R2.fastq.gz", "fastq fastq", 7170010275.0, 95600137.0, "GSM4812177 r1", "0:60 1:15", "A:1431609486;C:1054601932;G:1216286918;T:3467366696;N:145243", 60, 15, null, null, 1431609486, 1054601932, 1216286918, 3467366696, 145243, "SRX9221550", "SRS7455251", "SRA1136461", "GEO", "Junker, BIMSB, MDC", 2, 0.0612, 0.0, 0.02447, 0.0, 0.98612, 1.0, 0.67753, null, 60, 15, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "scslamseq", null, "Germany", "2020-09-30", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [61427, "SRR12749592", "SRX9221549", "SRS7455250", "SRP285948", "PRJNA666689", "Spatio temporal mRNA tracking in the early zebrafish embryo", "GSE158849", "Other", "We performed spatially resolved transcriptomics with sub single cell resolution in zebrafish embryos at the one cell stage  which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac  the vegetal pole. The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes  but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys  mature X. laevis and X. tropicalis oocytes. 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The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes  but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys  mature X. laevis and X. tropicalis oocytes. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf.", null, "pubmed:34099733", null, "tomo seq zebrafish replicate1", "GSM4812175", null, "tissue:1 cell stage embryo|strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen  cryo secti1d embryo.", "tomo seq zebrafish replicate1", "zebrafish tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode Genome build: GRCz10   release 90 Supplementary files format and content: csv file containing gene counts per section xenopus tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode and translate gene identifier to gene names Genome build: X. tropicalis v9.1 genome assembly  X.laevis v9.2 genome assembly Supplementary files format and content: csv file containing gene counts per section scSLAM seq zebrafish demultiplexing using cellranger mkfastq v3.0.2 mapping and whitelisting of cells with cellranger v3.0.2 splitting labeled reads >1 T C mutation from unlabeled into separate fastq files submitted to this GEO entry mapping with STARsolo v2.7.0f 0328 single cell analysis in seurat v3.1.2 Genome build: GRCz11 Supplementary files format and content:  barcodes.tsv list of barcodes   genes.tsv list of genes  and  matrix.tsv count matrix", "one cell stage embryo", null, "none provided by the submitter", null, "strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen  cryo secti1d embryo.", "GSM4812175", "GSM4812175: tomo seq zebrafish replicate1; Danio rerio; RNA Seq", "GSM4812175", null, "1", "none provided by the submitter", "GEO Accession:GSM4812175", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP285948", null, null, "tomoseq.zebrafish.rep1.R1.fastq.gz tomoseq.zebrafish.rep1.R2.fastq.gz", "fastq fastq", 5895274800.0, 39301832.0, "GSM4812175 r1", "0:75 1:75", "A:1689609675;C:789159514;G:1226360483;T:2187499981;N:2645147", 75, 75, null, null, 1689609675, 789159514, 1226360483, 2187499981, 2645147, "SRX9221548", "SRS7455249", "SRA1136461", "GEO", "Junker, BIMSB, MDC", 2, 0.79456, 0.13632, 0.05206, 0.00854, 0.85208, 0.99673, 0.63142, 0.73208, 75, 75, "B", "T", "mate2 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "scslamseq", null, "Germany", "2020-09-30", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 3, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "scslamseq", "p2": "Embryo Imprecise"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "cDNA", "label": "cDNA", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=scslamseq&tissue_curation=Embryo+Imprecise", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": 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"tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq&tissue_curation=Embryo+Imprecise", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=scslamseq", "selected": true}], 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