run_metadata
3 rows where devstage_curation = "Undetermined" and technology = "scslamseq"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 61426 | 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. | pubmed:34099733 | tomo seq zebrafish replicate3 | GSM4812177 | 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 | none provided by the submitter | strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen cryo secti1d embryo. | GSM4812177 | GSM4812177: tomo seq zebrafish replicate3; Danio rerio; RNA Seq | GSM4812177 | 1 | none provided by the submitter | GEO Accession:GSM4812177 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP285948 | 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 | 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 | 60 | 15 | T | T | mates < 9% mapping rate | illumina | nextseq | 3prime | cdna_unspecified | unknown | sc | single_cell_plate | scslamseq | Germany | 2020-09-30 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 61427 | 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. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf. | pubmed:34099733 | tomo seq zebrafish replicate2 | GSM4812176 | tissue:1 cell stage embryo|strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen cryo secti1d embryo. | tomo seq zebrafish replicate2 | 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 | none provided by the submitter | strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen cryo secti1d embryo. | GSM4812176 | GSM4812176: tomo seq zebrafish replicate2; Danio rerio; RNA Seq | GSM4812176 | 1 | none provided by the submitter | GEO Accession:GSM4812176 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP285948 | tomoseq.zebrafish.rep2.R1.fastq.gz tomoseq.zebrafish.rep2.R2.fastq.gz | fastq fastq | 5700594075.0 | 76007921.0 | GSM4812176 r1 | 0:60 1:15 | A:1648247694;C:1091850406;G:1097354943;T:1863017844;N:123188 | 60 | 15 | 1648247694 | 1091850406 | 1097354943 | 1863017844 | 123188 | SRX9221549 | SRS7455250 | SRA1136461 | GEO | Junker, BIMSB, MDC | 2 | 0.88481 | 0.0 | 0.03195 | 0.0 | 0.85794 | 1.0 | 0.80123 | 60 | 15 | B | T | sc-like readlen | illumina | nextseq | 3prime | cdna_unspecified | unknown | sc | single_cell_plate | scslamseq | Germany | 2020-09-30 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||
| 61428 | 61428 | SRR12749591 | SRX9221548 | SRS7455249 | 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. | pubmed:34099733 | tomo seq zebrafish replicate1 | GSM4812175 | 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 | none provided by the submitter | strain:AB wildtype|treatment:untreated|extraction protocol:Fresh frozen cryo secti1d embryo. | GSM4812175 | GSM4812175: tomo seq zebrafish replicate1; Danio rerio; RNA Seq | GSM4812175 | 1 | none provided by the submitter | GEO Accession:GSM4812175 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP285948 | 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 | 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 | Germany | 2020-09-30 | Undetermined | 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");;